Thanks for the very in depth review!
The selling was a last minute addition, originally there was not meant to be a way to manage placed tower but I've had many requests for the ability to move them. In lack of time I found it easier to implement selling at full payback as it is effectively moving (but it has the unfortunate side-effect of letting you convert small towers into big ones). Later jam polish is definitelly seeing the selling gone in favor of moving. This obviously had a detrimental effect on the difficulty scaling of the later waves as they were not properly rebalanced to account for the selling, but I favored polishing the concept over more playtesting to get the right difficulty.
Later towers having a limit of what levels they can target is there to encourage the use of the smaller towers (the Marker being a big AoE tower that *needs* smaller towers to trigger the marks also plays into that). I wish I polished the concepts behind the towers themselves better but in lack of time I had to rely on ideas that are simpler to implement, we'll see what will come of them in the post-jam polish from all the feedback I've been getting.