I have found that the two biggest problems specified are not problems at all. Let's take software for example, this is not a problem at all, in fact I have a good amount of options. If I am to buy a Mac, it will be of course a laptop, and it will be test computer. Because I will never let go of Windows, I will never buy (If it is free then sure) made for Mac software other then iLife, which you do not buy it comes with the machine. But because of my already established Windows machines already running my established library of software, I will not go out and purchase a new set of the same software ported to the Mac platform. Therefore several options come into play, I can run Windows in Bootcamp, I could run Windows in Parallel, I can run VMWare or VMware fusion(this is awesome software), I can run WINE, or Crossover Mac. All these Apps will allow me to mimic a Windows enviroment either virtually or through API Enviroment emulation. So software isn't a problem at all, whether I am using OS X or Windows which will be entrenched on the Macbook.
Secondly the hardware, this is probably the most compelling reason for me to buy a Mac. The OEM hardware out there just stinks. In my opinion OEM's make plastic boxes with no power to back them up, except for a few of course. Apple on the other hand packs the best hardware config I have seen into a laptop, as far as advancedment, in general I feel the config could offer more features, but it is great. And least of all importance to me the laptop looks great. Apple using only hardware they allow, although being a measure I don't generally agree with, does work for them, it allows their OS to be stable because it isn't rellying on third party drivers to keep it level on the hardware foundation.
So the two biggest problems mentioned I can work around. I am just trying to get all the deep down technical knowledge I can about the Mac. Because it does intrigue me how the OS works. Even the history of the OS and how it works intrigues me with the New/Old World Rom and the OS toolboxes.
And thank you rashidtem for answering my intial question about .app, you thus far have been very helpful.