Over on AMD's website, there's a support page that reveals the company will not honor warranty requests if customers used AMD processors in combination with any other heatsink/fan than the one provided within the processor-in-a-box (PIB):
Is the warranty for my AMD Processor-in-a-Box (PIB) still valid if I use a different heatsink/fan (HSF) other than the one provided in the PIB?
No. The limited warranty shall be null and void if the AMD processor which is the subject of the limited warranty is used with any heatsink/fan other than the one provided within the PIB.
Basically, this means if that your Ryzen processor shipped with a HSF, AMD may be within its rights to refuse warranty requests if they can somehow prove that you didn't use the boxed cooler.
ProClockers asked AMD for an official statement but hasn't heard anything back yet. It's definitely a weird policy, but there's no evidence of it being enforced:
When I first found this information, I didn’t bother about taking the source seriously. I went straight into searching the information on AMD’s site and found the FAQ page. Since then, it seems like this is a page that is in need of update, but is still active like it’s the current policy. At this point, I’m 99% sure that this policy was never being enforced and will be reworded for aftermarket coolers, but we’ll wait to update again after an official statement.