So it's okay to choose which of three different class combinations a companion has, what abilities they learn at level up, and what weapons and armour they use, but going beyond that crosses some invisible line of character autonomy?
From a designers point of view: yes.
Let me elaborate: the cRPG games tell a story, there is a plot and history to it. Because a companion was designed to be either a druid, or a chanter, or a mix between the two, I see it as a developers concept for that particular character. It makes no story-wise sense for that character to be a barbarian, or a wizard, or some other mix of two other classes. The design says that this character is what it is, so you shouldn't be able to change it.
You play a roleplaying game by roleplaying (duh). If you meet a druid/chanter character, then ACT LIKE you met a druid/chanter, because the story says he/she is a druid/chanter. Don't change the whole background on a whim, because it ruins the whole design. Viconia's story wouldn't have much sense if you could switch her into a bard, no?