Cavalary: And in Arcanum only the PC gains exp, with companions leveling when the PC does, hence that problem with them being below the PC's level when joining.
I hear that an obscure NES game called Legend of the Ghost Lion is also like this, which permanently penalizes the player for leveling before finding later companions.
(On the other hand, note that Legend of the Ghost Lion handles leveling up differently; instead of earning XP from enemies, you level up by finding a certain item.)
The Magic of Scheherezade handles this better. Companion stats are tied to the main character's level, and levels gained before the companion joins do count. (Worth noting that said game consists of discrete chapters with no backtracking between them; also, when you complete a chapter, you're automatically leveled up to the level cap for that chapter, which serves as the starting level for the next.)
Incidentally, this also reminds me of an issue that is found in Shin Megami Tensei: Nocturne and Geneforge 1 (not Mutagen); XP gained from battle decreases as the main character levels up. This means that companions (demons in SMT:N, or creations in Geneforge) who join (or are created) late won't have a chance to catch up level wise unless they start at a high level, which means you can't, say, train a new Pixie late game and expect it to be anywhere close to the expected level.
(On the other hand, one game that handled this better is Castlevania: Curse of Darkness. In that game, any companion that is lower in level than the main character will gain XP much faster, allowing said companions to reach a decent level in a reasonable amount of time. This means it is feasible to get a new companion up to a reasonable level if, say, you want to try out different types of fairy.)
vv221: I used to combine it with another mod doing only a small tweak: skill progress on failure instead of success, so skills progress quickly at low level and slow down at high level.
Reminds me of Wizardry 8, where failing to cast a spell gives you more chances for skill growth than casting the spell successfully. (Note that this is not the case for many other types of actions. Also, note that the manual explicitly mentions failure being good for skill development, so I would not consider this a bug.)