I don't get it, what exactly are any of those things supposed to do in your mind? They'd have absolutely no impact whatsoever on fly.

Like you do know that there is no height limit to fly, right? You can cover 12,000 feet total with one cast of fly. If you need to carry party members one at a time (Although even two at once is likely feasible via lift/carry rules even with a measly 8 str), at a standard party of four that's still 4,000 feet per person.

So, like what kind of tree canopys or smokestacks are you talking about there? Or just random invisible walls 3000 feet, the height of the burj khalifa, above the 1000 foot wide chasm simply so the wizard can't fly over it?

... And whatever it is that now has these absolutely astronomical dimensions, so clearly humungous that it is an immersion-breaking encounter designed purely to counter fly spell... If you can't cross it with fly, how else are they gonna cross it? Like, what else could the party possibly have up its sleeve to deal with this now, if even fly wasn't enough?

If your entire encounter can be bypassed by "I cast fly" it probably wasn't very interesting to begin with.

Well, that's just entirely subjective, I guess. I personally find needing to come up with creative use of the environment, items, tools and actual teamwork from the party always interesting. There's usually literally endless possibilities or solutions to even simple problems.