I don’t think it’s that much of a plot-hole, it’s fairly obvious to me that however Cosmos is Usagi, she’s not the Usagi from either this current timeline or lifetime, therefore it’s not a big leap in logic to assume that two forms of the same person being in the same space doesn’t disrupt the time space continuum unless those two forms are from the same lifetime/timeline.
Cosmos is either a completely new reincarnation of the Silver Crystal Star Seed or a Usagi from an alternate timeline where she gives into Chaos’s despair at the Cauldron and chooses to absorb all her Senshi’s Sailor Crystals into her thereby becoming “the Cosmos,” and technically an amalgamation of all the Solar System Senshi rather than merely Usagi herself.
Cosmos is either a completely new reincarnation of the Silver Crystal Star Seed or a Usagi from an alternate timeline where she gives into Chaos’s despair at the Cauldron and chooses to absorb all her Senshi’s Sailor Crystals into her thereby becoming “the Cosmos,” and technically an amalgamation of all the Solar System Senshi rather than merely Usagi herself.