I don't think anyone questions they need better position players. Whether the threshold is an .800 OPS or maybe something more along the lines of OPS+ based, this offense needs help.
I think Flaherty has pitched himself to a point where a trade return is going to be better than the qualifying offer compensation. Maybe that's debatable given his recent back issue, I don't know. I think he gets traded before the deadline. As fun as the Tigers have looked lately, its tough to see this stretch continuing given the pitching rotation health. They've given themselves a puncher's chance, but let's see how they get through Cleveland and Minnesota. The other issue is that they're chasing teams down, so they have to rely on their downfalls as well.
I think Skubal could still command a similarly high return during the offseason. I think he'll be kept unless the offer is too much to decline. I do disagree with what you said about replacing him directly. The Tigers can ask for a top tier pitching prospect as part of a trade package. I suppose we can debate whether or not that is a replacement for Skubal based on current value, and that's fine.
But they're also going to need to find some arms this offseason to begin with. Almost certainly in the bullpen, but probably more rotation depth as well.