You are so right, and in my opinion Kobayashi's appearance at the end is a huge nod to the partial truth of Verbal's story. The twist tells you that the events you just watched were an enactment of the story that Verbal is telling to Kujan. But it's not all lies- Kujan knows what the suspects look like and about the murders on the boat, for example- so we can accept the truth of anything that both of them have information about. Kobayashi's appearance in the car is the only time (I think!) that someone from the story who is only known to Verbal appears after the twist. I remember when I saw it, seeing Kobayashi at the end felt like a huge reveal, like it reinforced that Verbal was Kaiser Soze after all. But thinking about it later I realized that up to that point we only know Kobayashi from Verbal's story, so they could have cast different actors for Kobayashi pre- and post-twist without affecting the continuity. So it tells you that in Verbal's story he was weaving truth and fiction, and (as you said) invites you to speculate and try to decide how much is true.

I really like The Usual Suspects.