@priitv8 I want to respond to a few of your points but first let me say I appreciate your taking the time to provide a number options for consideration. Some I've already seen, some were new to me. As I noted above, I'll ultimately settle on something to work around this problem. That said...
How's the specific behaviour of OS X related to the price of the MacBook?
If I spend a premium price on a computer I expect both hardware and software to be commensurate with the price. Surely you don't suggest that the Mac pricing premium is based solely on the hardware. So, yes, I expect high-end laptop to be able to accomplish the same thing a $300 netbook can do: transfer junk-free folders to attached media.
Especially if the problem can equally well be attributed to the 3rd-party peripheral you've chosen to use?
No, this is a problem solely of Apple's making. A premium OS ought to be able to manage and present a users personal storage without mucking it up. Windows manages to do that and while Finder offers certain things not available in Explorer, the latter is considered by many to be the superior file management tool. In any event, it is not incumbent upon 3rd-party products to accept junk files.
Your suggested solutions.
Honestly, you can offer 100 or 1,000 different ways to solve this problem (and they'd be appreciated), but it does not change or negate this basic fact: this should not be a problem in the first place.
Secondarily, I find it offensive that Apple has arrogated unto itself the right to place hidden files in what I consider to be my property. A thousand ways to remove them (none offered by Apple) doesn't absolve that offense.
Anyway, I think we've gone around this enough. I appreciate the help. Notwithstanding my complaints, there a many things I like about the rMBP. I don't want to simply give up on OSX and run Windows, but at the same time I've got to call it like I see it when OSX blows it. When it comes to respect for and management of the computer owners proprietary data, OSX really blows it.