entity_load failure: Adding revision capability to entity with existing data and unticking "create new revision" still creates a revision
So I experimented and contrary to what I perceived, saving a node (as an example of an entity) even without "save a new revision" checked, still saves a revision...

So somewhere in the confusing bowels of the entity loading procedure it was diving through Drupal-shaped rabbit holes and trying to load revision information because it noted that the custom entity was revision enabled (where I enabled it in hook_entity_property_info). Because I'd only added the revision capability after using the entity there was none. So I had to do some SQL work.

Firstly I selected all information in the original table into the new table. In doing so, the auto-increment setup on the revision_id column populated the revision_id column in the revision_id with unique incremental values. 

Secondly I did a big ol' looping thing to get all the revision_ids from the revision table and one-by-one put them in the original table. Details of that query are here after I had a little bit of trouble, but it might help someone else out.

Now it's working.