Just mentioning that I had a similar experience when moving from 5.16 (auto-deployed by Digital Ocean) to 5.36. There are now around 60 tables. Note that for me, it was helpful to issue
use mattermost;
as the first MySQL command; otherwise, all the alter table commands failed.
My symptoms were the sidebar not working right, and errors in the Mattermost log mentioning new channel IR_Incident after Bleve indexing seemed to hang at 95%. I’m not convinced that the latter is fully fixed, but I believe it’s unrelated to the table collation problem now, at least.