Oh dear god here we go again ................... so the game will sometimes force you to put SP where you don't want just to be able to move on instead of giving you more diffcult or punishing ways of finishing the quests if you can't pass certain skill checks; without having to change your initial build, is that what you're saying?
There's always* a way to progress using one of your main skills, but there are skill checks you have to pass no matter what. The vomit endurance check for example. If you have 1 endurance, you'll fail unless you roll boxcars. Then you do some stuff and get one free retry, which you'll likely fail again. Then you get a Thought you can internalise, which dramatically improves your odds, raises the Endurance learning cap to 4 (it was 1 if your Physique is 1) and gives you another reroll (at that point your odds will be about even, assuming 1 Endurance). If you still fail, your only recourse is to put a pip in Endurance, which bumps your odds to about 2/3 and another reroll.
And yes if you're really unlucky you might have to do that a few more times, thereby ending up with a lot more Endurance than you planned. On the other hand playing with 1 Endurance is really hard because you only have one single miserable HP.
(There's a similar skill gate with Measurehead, on Physical Instrument or Rhetoric, but you don't need to do those if you've passed a couple of Perception checks elsewhere.)
So, yeah, you really might have to buy some skills you're not super interested in otherwise.
*
usual disclaimers apply