I may be misunderstanding you, but either your code runs or it doesn't.
It will run after the changes to the PLL and other really low level initialization.
But you may see subtle difference in timing of accessing the registers, for example. Timer counter read taking 3 cycles instead of 2 or something like this will not matter for most applications, yet you may be doing something really specific, in which case you will have to re-calibrate your code. Same with GPIOs. If you did bit-banging and relied on register write time for timing, then slightly faster write time will throw off that timing.
And obviously, the code that is not subject to wait states will run much faster, so all your busy wait loops based on nops will have to be adjusted as well.
What is that actually? You hand the RM to an HDL coder and ask him to emulate the config registers and the functional description?
Yes, you take the device, take the RM and write a bunch of test cases and tweak the IP until it passes all those cases. If you estimate significant market demand, it makes sense to spend time doing that. It is not that hard to do either. And it was done multiple times by different companies.
I know a lot of chinese silicon is designed by Western design houses.
There is no need for conspiracies. GD is a legitimate company with office in the US. If there were any questions about IP cleanness, they would be sued out of existence.