The Twilight Zone licensing is pocket change compared to the cost of redoing the attraction (properly, at least).
Mostly Disney has been content to keep paying it for the attraction and simply sell merch without TZ branding so they can keep that cash for themselves.
In the case of DCA's Tower, the attraction was redone because its GSATs were low for what was meant to be a marquee attraction - ask guests what they came to DCA to see and almost no one said Tower, despite it being something many did once there.
Add the fact that DCA's Tower was always known to be the less-precious cousin to WDW's, the strong desire to get a new major attraction opening in the park, the interest in getting Marvel quickly into the resort, Guardians having a movie coming out on a timeline that a retheme could be completed by (but a newly built attraction would take too long), the limited space in the park, the success of the first movie indicating the sequel would likely do well, and the property being suitable for a thrilling attraction and you have the basic recipe for why their Tower was reworked. Many have theorized it's because Disney wasn't interested in paying the Twlight Zone licensing fees, but that was so low on the list of reasons it was basically negligible.
Mission Breakout wasn't exactly cheap, but it was fast, synergistic, and turned the facility back into one that was massively popular and actively pulled people into the park. The WDW Tower, meanwhile, has always been massively popular and a significant draw for the park. Something would have to shift noticeably for WDW to gain real interest in retheming.
A new hit movie based on the ride could be enough to do that, but whether the movie will be a hit remains to be seen.