yes, it seems to be something Gigabyte has implemented since z86 motherboards. I've googled it, and I've been unable to find real Gigabyte support answers to this topic, but, I've found other topics, of people arguing about the same behavior in their z86, z97 and x99 motherboards.
I've open a ticket on Gigabyte Technical Support, asking them if this is the expected behavior, and they have scaled the question to a technician level, since they only know this "if it works, then its fine", and I would appreciate a proper answer about this.
Lately I've been thinking about this, and discussing it with some friends, and we got to the point, that, It can make sense what gigabyte has done here, to have the bottom gpu's detected has the primary, because, "usually" the primary gpu is the most used, hence, it seems reasonable that, the most used gpu, should be located at the bottom of your case, where fresh air is found, and so, it will be the most cooled gpu, and will have more space left for boost.
It also make's sense, that, Phyxs is now working by default on my 1st gpu (the bottom one) so, I think this something gigabyte / nvidia has intented to do. (On my previous pc, with an asus x58 motherboard, the bottom gpu was detected as GPU2, and physx was by default set to this card)
What do you think?