I don't see how it being PvE or PvP really makes a difference. In game design in general balance is a key concern, video or otherwise, multiplayer or otherwise.
To go back to the CRPG example, if I'm playing a game by myself I would still like different classes, as well as the various abilities of those classes, to present interesting choices to me as a player. Characters and skills tend to have pros and cons and aim for vague parity in terms of efficiency and fun, while catering to different tastes and tasks. It's a fairly big undertaking and some games put a lot of effort into it. Arguably perfect balance is unachievable, but that doesn't mean we should stop trying. There are extensive balance discussions relating to single-player games too, Devs don't want to spend time programming multiple classes if players are then going to gravitate towards just one.
If it's 100x more effective to play a wizard, then people choosing not to be a wizard have to make a conscious choice to handicap themselves IRL - knowing the rules and limits of a game and choosing to ignore them. They can do this, but it's not desirable design-wise. Similarly, if a wizard has one extremely powerful spell that does everything and has no drawbacks that's detrimental to variety regardless of how many other spells have been programmed in. Putting them in the game isn't the same as making them useful.
The motivation would be to make the game better, in part in the terms I've just described. They've already done several balance passes in the game's lifespan and will probably do more. The suggestions forum exists for people to make this kind of request.
The thing is, you started out by saying "these ships are great", but now as far as I can tell you're accepting that they aren't in comparison to others, but that's fine because you don't care? There's a subtle but important difference between defending a piece of game design or just saying that you don't care about it - but yeah... I might be missing some element of your case here, and I can see we're not going to see eye to eye on this and that is, as you say, fine.