Homunculi can't get past 99 while you are Alchemist/Biochemist, once you become Geneticist they will be able to level further.
BUT! If you let them go past 99 w/o turning them into Homun S first, they will lose potential stat gains. That's why Geneticists keep them Vaporized at level 99 until they do the Homun S quest. (They keep getting exp at 99, so once the level limit is raised when you turn Gen, a random kill might make them level up)
Basically, the homun leveling path is:
Baby Form + Loyal -> Use Stone of Sage to mutate into Mature Form, (But due to how Loyalty works, your homun can reach lv99 way before being Loyal)
then
Mature Form + lv99 ->Turn to Homun
As ShoLin stated, if you want the Loyalty Skill you'll have to re-Loyal it in Mature form again....but keep in mind that once you turn it Homun S, loyalty drops...again.
Honestly, I don't see much use for the Loyalty Skills of Filir and Vanilmirth (what's worse, using them resets the Loyalty to Hate), Lif's I really don't know about. I got Bloodlust on my Amistr...because that's what others told me, I reckon it helped it level a little faster though.