Hello Hahn and thanks for asking this!!!
Setting up the right gear...really hard task indeed.
Man will go over and over,buying new stuff and it goes forever.
You said it well,pickups aside the guitar is purely about personal preference and comfort.
But I guess that is the same case with amp as well.
Each of us has different taste,needs etc so straight recommendation is wrong way,imo.
You mentioned versatility and I'll stay on that one,cause I do play many stuff and need guitar of wider range.
As you probably noticed,I play Musicman Axis a lot,it has 2 HB.
Now,when I got it,I was totally amazed by high output,lots of bass and midds,almost like LesPaul,pure power.
But also,Mark Knopfler is one of my fav players and I just couldn't get that crispy,single coil tone.
So I splited pickups and I'm sort of satisfied with it.
Main sound for stuff like Knopfler is 4th position of 5 way switch,combination of neck and middle pickup(all singles of course,Strat feel)....and I have 2 HB on Axis,3 way switch.
Now,my new custom guitar shall be done in few days and combination of pickups is HB S S.
Neck pickup is really high output type,but combined with warm middle will produce sound I need.
And plus passive pot in tone position with 5 different EQ cuts,just in case if I need more power in neck pickup.
Still, the best option for full versatility is HB S HB,sort of Suhr Govan model or som like that.
And that's not the end of story,wood is really important matter here,plus amp,cabinet etc.
This is just my opinion,and suggestion is to try as many combination as you can.
And I can't promise that you will stop once it for all,if you find gear you like.
That request goes forever,same as music.
Exploring,no boundaries...that is all about.

Hope this helps Hahn,tell me if you have more questions.

Take care