While I was totally stuck with this problem yesterday, I think I figured it out. I wasn’t finding the answers I needed because I was looking for help with blend modes. The problem was actually with the cropping filter. I found the answer here:
https://forum.shotcut.org/t/cropped-videos-wont-overlay/11691
Basically, if you crop videos for an overlay, the padding alpha channel has to be set to 0.