There was a posting from r.a.c.m.xbooks on usenet from years ago on just the subject of how Pheonix can be a singular entity across the multiverse while still appearing in What-If stories that may be useful here. (As characters from a Terry Pratchett novel would say, it's a very good description, even though it's probably completely wrong in all particulars.)
Think of multiple universes as a stack of papers.
The mundane progression of time can be thought of as running in a line along the x-axis across each of those papers. When a reality splits into a divergent timelines, those timelines spread out over the sheet across the y-axis. And of course each universe is stacked on top of each other along the z-axis.
As per the Cross-Time Caper in the early _Excalibur_, Pheonix is a unique entity in the mulitiverse, and for this model it naturally exists on only one universe sheet, on one level of the z-temporal axis, at a time - even though it can travel between them. Nevertheless, the Pheonix has been shown in several alternate reality stories, so presumably its existence can easily 'smeared' across the y-temporal axis. Presumably the 'unique entity' aspect means that the temporal divergents are somehow still parts of the same being, but this is where the theory strats to get iffy - especially if it has split off temporal divergents existing in multuple universes