>>58363050JP RT doesn't really offer any new information that contradicts the English release, for the most part, so it's likely 3 from your list to avoid narrative inconsistencies. It is stated though that Ninetales has 神通力 (jintsuuriki, divine powers) rather than simply "psychic powers" which imply more of a supernatural element to the story, but that's mostly irrelevant.
On Explorers, I'd assume the three main time travelers all come from the same world if the rule of PMD's time travel doesn't normally run on multiverse. It's implied that when the past is rewritten, the future before that change ceases to exist, with rare exceptions (Protag being a lone exception in main story, with Dialga being the one to do so, also causing the "space time distortions" Luminous Spring and later both fake and real Cresselia mention, and Arceus being implied to save the entire bad future world, only after almost fading away). If we go by the rule that rewriting timelines means that the old one ceases to exist, then they can only come from that one bad future timeline. It's also worth noting despite the planet being paralyzed, the "time travel" between present and bad future seem to function on consistent time points, since the chronology of the protag, partner and Grovyle being trapped and returning has them being missing during that period of time in the present, with Bidoof/Sunflora's diaries making explicit mention of their absence.
>Can you even be born when the time is frozen?This one seems odd, but I chalk that up to inconsistent writing. When the Time Gears are stolen and the flow of time is stopped, characters like Mesprit mention that if you're caught in the paralysis, you're also frozen to time, so Pokemon even existing in the bad future becomes an anomaly.
Back on the human topic, I personally think based on the info presented in the games, that they existed at one point, but almost all traces of them barring the Explorers protag become almost nonexistent after RT.
