So I figured out the majority of the problem.
1. if it won’t rate stretch, which seems to happen often enough, just change something about the clip like turn the effect on/off. Maybe click on another one, then come back. This has worked every single time other than clips with transitions on them.
2. transitions. By default, you’d think you can’t change the rate of those clips. But wait, there’s more! You literally have to put your mouse in the Tiny space in the clip between the top or bottom of the clip on the timeline and the effect itself. With that mouse pointer, it’s somewhat difficult to tell where that point on the mouse is, and you get No feedback as to whether or not it’s going to work. But you can just make that row in the timeline taller. (you can hold alt and scrollwheel over any part on the left side of the timeline, which is easier than trying to move the edge manually).
So it seems no part of my workflow is actually causing a problem. It appears that there May be a bug because in most cases, a clip will stretch after simply turning something off then back on again. What it Actually appears to be are a few poor UI choices by Adobe (no big surprise). One example of poor UI choices is just looking at AE, PR, and Audition. They All have timelines, but all 3 have different interactions for moving around the timeline.