JT was the one they never put on IL, they kept thinking it was going to be less than 10 games and then it was almost exactly that. Marchan had come up on September 13th and JT returned on the 22.
Hoskins actually did go on the IL but I see what you mean - he never actually came off it, "activated" only for end-of-season housekeeping.
It's kind of funny to think that Klentak really only got fired because the team didn't make the playoffs as they probably would have with those two guys healthy. I don't know that a 7th-place finish in a fake season would have been good enough, unless they'd won in the first round as well, but I do think it was mostly a PR firing - especially given how close they came to just letting MacPhail and Rice run things this year - and admitting the entire system was a problem only came later.
I would say that one way or another, Dombrowski is going to have to trade a current starting position player this off-season. Hoskins is the easiest guy to trade. Bohm would be the most controversial (but still probably the most valuable and you can't rule it out). Segura would be the bold choice (gambling he won't be as good while being able to get a better deal for him than you could for Didi). Or Didi. All four of those guys need days at DH and so does JT and Harper.