IANA spokesperson for FIDE, but I’m not sure you have this correct. As we’ve been discussing in the concurrent but less suitable for this topic Pit thread, the new rules seem to be trying to formalize FIDE procedures for recognizing gender identity changes. The rules in question are here.
The two-year limit applies AFAICT not to the overall validity of the new rules, which are not in fact being proposed as “temporary”, but to the time that FIDE may require to verify the official status of the player’s gender-identity change.
I don’t think the two-tiered chess competition system is attempting to conform to any speculative theories about innate inferiority of women in chess skills or anything like that. As I said in the other thread, “AFAICT there are ‘open’ competitions and ‘women’s’ competitions. The idea seems to be, as in women’s poker tournaments and similar, that the massive underrepresentation of female players at competitive levels makes it more attractive for female players to have women-only events.” In chess in particular, it seems to be a historical legacy from the days when women had almost zero representation in chess competition.
As for the asymmetry in what happens to pre-transition competition titles for a transgender players, quoting myself again, “the assumption is apparently that one’s transgender identity is considered to apply retroactively, and thus a transgender man shouldn’t have been competing in women’s events in the first place.” But a transgender woman keeps any titles that she won in the open competition categories while identified as male, because anybody’s allowed to compete in the open categories.