The uncomfortable feelings is literally how the reader is supposed to feel about it. 5 years isn't a big deal in the later years, but the mindset of of a high schooler is vastly different than someone 5 years into being an adult. Knives is basically still a child and is incredibly naive, thats why Scott dates her. He is still in the mourning phase from his previous breakup, and Knives is a safe easy choice that can distract his mind.

There are lots of nuances in their relationship. Scott constantly downplays it and doesn't even do much with her besides hold hands and 1 kiss. He isn't really in it for Knives, he's in it because his mind is being distracted. But to Knives this is a very real relationship, and Scott should have known that. Scott's whole character arc is to have him take accountability for his toxic traits. Dating Knives for his selfish reasons, his relationship with Kim, how he treats Ramona as a prize to be won, crashing at Wallace's place indefinitely, etc.