Definitely agree on them being a default option. I fail to the see what's at stake here, what balancing it would break (aside from the anecdotical matter of additionnal slot added for these, easily fixed if that really is a thing).
Nobody cares if you autodock or dock "like a real man", it won't affect anything. Although I prefer docking manually, and I remember being rather against the autodock modules when they were introduced - because in 2014, docking felt like a very important part of the game, as focus was very much on the flying mechanics -, now I feel these modules are an artificial gamy limit with no particular purpose.
I've always removed these modules (except planetary landing oc), I don't see the point of sacrificing a slot for them (maybe because I don't fly T9 or Cutters), I'd rather have a fuel/repair limpet controller or 2 tons of extra cargo space. But I understand those who appreciate the comfort.
You need to know how to dock mostly for smuggling... Also, there used to be the issue of the broken canopy, but it's no longer relevant as synthesis and mats give you more than enough time to enjoy the luxury of relying on autodocking.
No really I can't find a situation in which your preference regarding docking method would matter.
And I kind of feel the same about supercruise assist, though I haven't used it enough to be sure about this one. The one time I did, I didn't get the point, but I didn't dig into it that much.
NOW from time to time, for RL reasons, I wouldn't mind having the option of autodocking just to be able to take a break from the game (go make tea, check mails, etc.) ; it would make things a bit more fluid. But not worth it InGame.
I personnaly feel they should be default in every ship as a QoL improvement. As an in game balancing thingy, err... It's pretty much hollow.