I think method B is a lot less risky and that's the one I use for all of my rigs.
Method A : "It is risky to supply the motherboard and some risers with differents PSU. But supplying a GPU and his Riser with differents PSU is ok"
I don't think that the motherboard has any reasons to care about how you powered the risers. You only connect them together with the data cables ("usb"), it's a very low-power connection as far as I know. A gpu, on the other hand, can draw up to 75W from the riser, and a lot more from the extra 6/8-pin pci-e connectors, so it might not like the power coming from different sources.
But I don't have (obviously

) a deep understanding of this so also interested in others' opinions.
Make sense to me. Still a lot of people doesn't agree
a shop site saying "Warning: do no connect motherboard or risers to the secondary PSU")