As far as i can tell, the platform is still Open, and well documented. This is good because it'll alow Amiga Inc to control the copywrite of AmigaOS as well as let developers port their Operating Systems to the platform easily, unlike Apple hardare.
Having a custom ROM does sound as if it could just be adding custome hardware. But as i understand, this isnt a big part. It just replaced the OpenBIOS and this isnt used by the operating system. So it shouldnt have an effect on porting of OSes or anything of the kind!
So its still very open. Anyone can make an AmigaOne machine, they just have to pass Amiga Inc Quality Checks. - Kinda like an ISO Quality Audit, only an "Ami Quality Audit"

.
I dont think its going to be a big deal. If it ensures quality with AmigaOS, good one em

. If this improves performance of AmigaOS, good on em

...