After considering this a bit more, it seems like there are some ways to make it work without breaking lore (except the transformation issue, which I have no solution for):
The DP would give new players a common base, a starting point from which to RP if they don't have any (clear) idea of the lore and their character. IOW, they're mostly clueless and that's brought IC, instead of a lore dump. The DP shows past events that may or may not help with RP, but can be tied together when discovering more lore.
The timeline aspect is interesting but the DP itself may hold the solution: the "otherworldly threat" that pulled the PC out of the portal lane, combined with Voduls intervention, may add completely arbitrary delays in the travel time, with the PC held in stasis during the transition. So it may be that everyone went into the portal at about the same time, but some arrived instantly (without visiting the DP) while others got delayed a couple of centuries. Would work for me, except that would mean that either portals themselves don't have uniform travel times or the "otherworldly threat" would have been lurking since the beginning, snatching only some. From the portals ingame, it seems transition is instant, but that's only inter-Yliakum, and maybe intergalactic travel isn't.
Problem: Kran and Lemurs would never go to the DP (Lemurs might, for Laanx has messed with them quite a bit, but would have noticed random delays, but maybe didn't care if a few were lost in transit.).
That people come from the portals more or less regularly seems to be canon though since dedicating an entire outpost to their guidance would be more akin to SETI otherwise. Except there is no reflection of this in the ingame lore I've encountered yet, but things may start to unfold at later stages, possibly after all the original questlines.