Earlier quoted context omitted.
It's more a matter of principle ? IMHO it should be illegal (for a for-profit corporation) to own both the OS and an application store (at least the kind featuring third-party software) - you cannot expect them to be a fair judge of who gets in there and who doesn't !
You can still run the software, but Apple make it harder to do so (you probably have to Google how to do it). You could argue this both ways, I think there's value to the defaults making it harder for your average user to run software which could be unsafe... just think how bad the malware problem used to be on Windows for example.
The malware problem used to be bad on Windows because everything had admin access. And the later "we don't have this program in our database, do you still want to execute it?" dialog wasn't too bad (especially when paired with an integrated blacklist of known malware !).
And why do you assume that other software distributors than OS makers aren't going to do due diligence ?