I don't know about the Penal laws not being directed at the Pope, I looked at part of the link and found a few examples which I listed below:
And for as much as great disquiet and many dangerous attempts have been made to deprive their Majesties of the said Realme of Ireland by the liberty which the Popish Recusants there have had to sit and vote in Parliament, no peer of that realm shall vote in the house of peers, nor shall any member of the house of commons vote or sit during any debate until he take said oaths and make the following declaration against transubstantiation.
This oath said: "I, A.B., do solemnly and sincerely, in the presence of God, profess, testify, and declare, that I do believe that in the sacrament of the Lord's Supper there is not any transubstantiation of the elements of bread and wine into the body and blood of Christ at or after the consecration thereof by any person whatsoever, and that the invocation or adoration of the virgin Mary or any other saint, and the sacrifice of the mass, as they are now used in the church of Rome, are superstitious and idolatrous.
And I do solemnly in the presence of God, profess, testify, and declare, that I do make this declaration, and every part thereof, in the plain and ordinary sense of the words read unto me, as they are commonly understood by English Protestants, without any evasion, equivocation, or mental reservation whatsoever, and without any dispensation already granted me for this purpose by the pope, or any other authority or person whatsoever, or without any hope of any such dispensation from any person or authority whatsoever, or without thinking that I am or can be acquitted before God or man, or absolved of this declaration, or any part thereof, although the pope or any other person or persons or power whatsoever, should dispense with or annul the same, or declare that it was null and void from the beginning.".
Then there was: An Act to Restrain foreign Education
Sec. 1. In case any of his Majesty's subjects of Ireland shall go or send any child or other person beyond the seas to be trained in any popish university, college or school, or in any private popish family, or shall send any money for the support of any such person, then the person sending and the person sent shall, upon conviction, be disabled to prosecute any action in a court of law, or be a guardian or executor, or receive any legacy or gift, or bear any public office, and shall forfeit all their lands and estates during their lives.
Same act: Sec. 9. Whereas it has been found by experience that tolerating at papists keeping schools or instructing youth in literature is one great reason of many of the natives continuing ignorant of the principles of the true religion, and strangers to the scriptures, and of their neglecting to conform themselves to the laws of this realm, and of their not using the English habit and language, no person of the popish religion shall publicly teach school or instruct youth, or in private houses teach youth, except only the children of the master or mistress of the private house, upon pain of twenty pounds, and prison for three months for every such offence.
Then there was: An Act for the better securing the government, by disarming papists
Sec. 1. All papists within this kingdom of Ireland shall before the 1st day of March, 1696, deliver up to some justice of the peace or corporation officer where such papist shall dwell, all their arms and ammunition, notwithstanding any licence for keeping the same heretofore granted. Justices of the peace, mayors, sheriffs, and chief officers of cities and towns and persons under their warrants, may search and seize all arms and ammunition of papists, or in the hands of any persons in trust for them, wherever they shall suspect they may be concealed. And such arms shall be preserved for the use of his Majesty.
Same act: Sec. 3. Every papist who shall have or keep any arms or ammunition, or who shall refuse to declare what arms or ammunition they or any other to their knowledge shall have, or shall hinder the delivery thereof to the said justices, or being summoned, shall refuse to appear or make discovery under their oath, shall forfeit, if a peer or peeress, for the first offence, one hundred pounds sterling, and for a second offence, suffer praemunire*. If such offenders are under the degree of peer, they shall for a first offence forfeit thirty pounds and suffer imprisonment for one year, and until they pay the penalty, and for a second offense, incur the penalties of a person attainted in a praemunire. The penalties and sums forfeited shall go one half to his Majesty, one half to the informer who shall sue for the same.
Source: *Praemunire: "that from the conviction, the defendant shall be out of the king's protection, and his lands and tenements, goods and chattels, forfeited to the king, and that his body shall remain in prison at the king's pleasure..... Such delinquent can bring no action for any private injury, how atrocious soever, being so far out of the protection of the law, that it will not guard his civil rights, nor remedy any grievance which he as an individual may suffer. And no man, knowing him to be guilty, can with safety give him comfort, aid, or relief." Blackstone, vol. iv, p. 117-118.
Then there was: An Act for banishing all papists exercising any ecclesiastical jurisdiction and all regulars of the popish clergy...
Sec. 1. Whereas it is notoriously known, that the late rebellions in this kingdom have been promoted by popish bishops and other ecclesiastical persons of the popish religion, and forasmuch as the peace and publick safety of this kingdom is in danger by the great number of said the clergy now residing here, and settling in fraternities contrary to law, and to the great impoverishing of his Majesty's subjects who are forced to maintain them, and said the clergy do not only endeavour to withdraw his Majesty's subjects from their obedience, but do daily stir up and move sedition and rebellion , all popish archbishops, bishops, vicars-general, deans, jesuits, monks, friars, and all other regular popish clergy shall depart out of this kingdom before the 1st day of May, 1698, and if any of said ecclesiastical persons shall after that day be in this kingdom, they shall suffer imprisonment, and remain in prison until transported out of his Majesty's dominions, wherever his Majesty or the chief governors of this kingdom shall see fit, and if any person so transported shall return, he shall be guilty of high treason.
An Act to prevent Protestants intermarrying with Papists
Sec. 1 cont. Any protestant minister or popish priest or other person who shall join in marriage any protestant woman without such certificate shall for each offence suffer one year's imprisonment, and forfeit 20 pounds, one half to the king, one half to the informer.
An Act to prevent Papists being Solicitors
Sec. 1. Whereas by experience in this kingdom papist solicitors are the common disturbers of the peace of his Majesty's subjects in general, and whereas there are great number of papist solicitors practising within the several courts of law and equity, by whose numbers and the daily increase of them, great mischiefs are likely to ensue, no person shall practice as a solicitor or agent in any suit in law or equity, who has not taken the oaths of allegiance and abjuration, and subscribed to the declaration against transubstantiation.
There are more examples, but this post is already too long.