The BIT/bool combination should be fine.
We have not tested with Connector 5.1.x. It is still in beta. I'm surprised you can generate from it in MyGeneration since, according to their release notes, they have changed the way certain aspects of the schema are reported. I thought it may have broken MyMeta.
We've looked at a lot of database conversion tools, each with pluses and minuses. They all have their restrictions, like some not converting FK relations, or SPs, or Views. I always seem to fall back on exporting CREATE TABLE, SP, and View scripts, and then doing a lot of search/replace in a text editor.
I usually start with MS SQL and convert to other DBs, so do not have a lot of advice to offer. I believe MySQL's Migration Wizard goes from MS SQL, but not back the other way.
David Neal Parsons
www.entityspaces.net