I personally like the idea of having things outside my playing field. If done correctly it makes the NPC more special. While we could debate him as a character I really liked Haer Dalis from Baldur's Gate II. His class most certainly wasn't off limits but his race, Tiefling and his twin swords most certainly were.
I suppose an issue might arise if it's TOO appealing though. I always wanted to cast spells like Irenicus did in those cutscenes but alas I was only part god and that just wasn't enough.
And he's a good example of my view: being a tiefling makes Haer'dalis cool, and gives him a few minor bonuses, but there's no mechanics that you can only explore by having him along. If you want a bard other than Haer'dalis, though, your MC can be that bard, and the main thing you'll be missing out on is his character and a couple of cool swords. A similar case in Deadfire would be Xoti, whose unique priest subclass is interesting and distinctive, but has little in the way of toys that only she can access (IIRC, all of her bonus spells other than Blessed Harvest appear on either the Priest of Eothas or the Druid ability list). You can't build another character exactly like Xoti, but if you see a mechanic on her that you really like, you're not required to have her along to use it (except for Blessed Harvest, which I'm okay with).
A counterexample would be Pallegina (in either game, incidentally), whose unique paladin order opens up an interesting alpha-striking playstyle that no other character can pull off. I personally like Pallegina and almost always have her in my party for that reason, but if I disliked her, I think it could be frustrating to be locked out of exploring those mechanics. In PoE1, if I want to mess with something like the Fire General, Pallegina is non-optional. Likewise, in Deadfire, something like the Tuono e Fulmine is locked to her character and requires I include her in my five-man squad.
Again, this isn't to say that companions shouldn't have unique junk, it's just to say that I think it's best if that unique junk isn't too different from what's otherwise available.