Yep, I found the problem. The entity limit is the limit of entity definitions. i didn't realize that there even was a limit on that. I thought this was a limit on entity instances. Which, on reflection, was a silly belief. Anyway, I added a mod setting: Maximum research level. I had originally set it to 100, but that causes 10,000 entity prototypes to get created. Instead, the new default is 25, which will only create 625 prototypes.
The reason so many prototypes are needed is because every single level of research for either size or recharge rate needs its own electrical interface. Thus, 25 levels of each research is 25^2 entity prototypes needed.