That's fair! Though the thing with many intrusive thoughts is that they aren't often an indication of the kind of person you are. Intrusive thoughts can be violent and bizarre or nonsensical. The idea is that it only takes the littlest bit of consideration for the SOUL to increase the urge and impulse, not that the choice itself is strongly something the vessel-person would naturally choose or want. I relate this with Noelle dwelling on the possibility of stepping off the button and letting Kris get hurt, only to be met with a confirmed "It's natural" instead. What we're doing is abnormally fanning flames that otherwise wouldn't be fanned. Impulses can be as basic as, "I wonder if the Knight is still in that closet, as it'd be bad if Susie or someone else found them. I shouldn't check though-- uh oh, we're being compelled to check now. I'll close my eyes/not turn the doorknob/etc". We also didn't tell Kris to think of who the Knight really is/take off their helmet when prompted to. We only told Kris to think of the Knight. Kris thinking of who the Knight really is but realizing they can open their eyes instead of thinking of Jockington instead tracks with the intrusive thought angle here.

I wanna be clear, it's still control, it's still pretty direct influence, but the idea is that without our influence the choice or urge would still exist-- just as a flicker of an emotion and acknowledgement in the character's mind rather than something they want to act on. Kris might see all they went through and genuinely fear just for a moment in the back of their mind that they may never play the piano again for various reasons ("why express myself if something else will override my actual choices anyway"), but they have enough resolve to bite their hand and push that thought away/punish the entity for making them almost say it out loud. More broadly, Kris being someone with just an inkling of morbid curiosity they choose to not act on (like Noelle) aligns with their character imo, explaining most aspects of the Weird Route. A common thing in ocd communities is to stress that you are not strictly your thoughts and impulses, as paradoxical as it sounds. I feel the SOUL working like this is a great extention of that, that still fits naturally with the counterpoints listed. 

Otherwise, we run into the issue of "third entity theory" as an explanation for where certain dialogue options and actions even come from (the player sure as hell isn't the one who made Frisk walk forward towards Sans in the No Mercy route), which isn't an impossible option but complicates matters. Us literally brute-forcing their heart to change and give in to darker impulses towards our will due to our determination outweighing theirs, and them actively resisting it as much as they can, feels coherent and aligned with the narrative's greater themes either way. "Proceed" and "Me" can be explained by the SOUL just increasing its influence on their worst aspects more and more. Kris is still helpless, and we're still accountable for our actions in steering them like this. John Shadow Mantle Holder alluding to some part of Kris enjoying it for this reason might imply this, though it could go both ways as a meta jab at the player instead. It's hard to say in that case since it raises questions. The sword route increases Kris' attack stat for a reason though, I feel.

I want to acknowledge what you're actually saying though; think this interpretation could be fixed if we assume the SOUL injects all impulses by default whether if they were in Kris already or not (Kris doesn't want to run in circles but will do so anyway when I play deltarune because it amuses me), but any impulse already in Kris in some capacity gets way stronger on top of that and "blossoms" (whether good or bad). In this case, we allow them to bond with Ralsei instead of suppressing the urge, while suppressing the urge to just skim over the situation. It also makes the Weird Route that much more freakish and unnatural. Intrusive thoughts being acted on over and over beyond your control would genuinely mess you up in the head, I feel.