I don't like your argumentation.
Anyway: if I get you right, you want the development of MC to put MC13.exe into their program folder and tell all the users they shouldn't be to lazy to type the whole path or use a BAT/CMD file?! I bet, my mother, my girlfriend and my father doesn't have heard of a BAT/CMD-file. And they even don't know the path of any of their programs. BUT they ARE able to use the MC13 comands, because MC13.exe is in the system32 dir.
If you're working with large corporations as you said, I guess you have a hard job. A good suggestion in this case here would have been: put MC13.exe in the program folder and make a registry entry so that all "MC13" comands will continue working without giving the complete path. Then I and all the other enduser could stay lazy.
Another point:
Not one other app I know of does this... and I've used so many over the past 15 years
I think I have many programs putting their files in the system dir! Sadly, I'm not at home and only have my laptop with a very, very essential list of installed software, so I only can give a few examples right now. I can give a bigger list later, if you want me to.
Let's start: First, I don't know what kind of OS you're using. Cannot be MS 95/98/ME/2000/XP/Vista. Because if you take a look in the System32 dir you'll find MS-Prgrams in their. Of course, there are system programs in there, but also:
mspaint.exe
magnify.exe
notepad.exe
soundrecorder.exe
But perhaps you'll tell me, MS can put in there what they want, because it's "their" folder let's take a look at other applications putting there files in there, perhaps you'll find some exotic, completly new programs:
QuickTime.qts from apple
TUProgSt.exe from TuneUp Software.