I also have a PPC board in my Amiga... But that is an Amiga... What we are talking about here are new machines, is there any difference between a x86 based motherboard and a PPC one in an "Amiga" case?
I meant a PPC board as a SAM PPC based board.
My A1200 BlizzardPPC was still an Amiga even when I took it out of its case and put it in a tower and it was running OS3.9.
My SAMs are Amigas even if they are in a generic £30 mini-itx case.
A PPC based MAC would still be an Amiga when running an Amiga OS although the tight connections to Apple would make this slightly more difficult to acknwoledge but still...
My SAM runs OS4 not Linux, not Windows nor OSX. You can run Linux on a SAM but at this point I wouldn't call it an Amiga.
So to answer the question...yes there is a difference. The difference is based on the OS you run. If the PPC motherboard is running YDL in an Amiga replica case then it is not an Amiga in my opinion. If the x86 in an Amiga replica case is running an Amiga Operating System then it is.
You can start going deeply into what makes and what doesn't make an Amiga but it would all be based on conjecture. What makes an Amiga OS more Amiga than another one? I have used and still use all the AmigaOS spin offs and out of all of them OS4 feels AmigaOS.
As it stands my above description fits my belief.
@Daedalus
I agree with you. I am running OS4 and, to me, it feels the natural and spiritual successor of AmigaOS. When I sold my A1200 BPPC 060 60MHz and PPC 266MHz with all the bits and bobs, Mediator, Voodoo 5, Soundblaster and OS3.9 and started using OS4 on my SAM it felt as I never left. I am not sure if it's clear. It doesn't feel alien. It's just faster than my A1200. Even the crashes feel original!

I always thought :"My A1200 has pc stuff in it...Voodoo, PCI, Soundblaster...but it's still my Amiga", the SAM is the same but it feels and it is Amiga to me at least.
I have loads of PCs and one runs Windows and goes straight into WinUAE, you hardly notice Windows is there, but you know it isn't Amiga.