I actually have no idea about the low level challenge. For speedruns I don't think there's a single category where we even have Ann join our party at all. But glitchless runs (at least on the gba version) typically finish with Ninten at lvl 25 and Loid at around lvl 4

Using glitches the lowest recorded level to beat the game is level 13 ninten/level 1 loid. Glitchless is level 25 ninten/level 1 loid. I also one time attempted a pacifist type playthrough where i only gained 2330 total experience across all 4 party members, mostly through bonus swooshes

I believe 13/1 or 13/no loid w/ glitches and 25/1 glitchless is possible across all versions (except NES doesnt have a glitched route) and is done in the current TASes