I'm upgrading from Commerce 13.32.5 to 14.5.0, and one step is to upgrade ASP NET Identity. There's a built in migration for this, located in EPiServer.Cms.UI.AspNetIdentity.Schema.AspNetIdentitySchemaUpdater<TUser>. However, this script does not work if you're targeting the Commerce DB, due to it also including transactions to tblBigTable, amongst others.

I don't have to store users in the Commerce DB, but now that it is the current case - I want to continue doing so. Also, if this is not supported - you should update Foundation to account for this, as that project also uses the Commerce DB for ASP NET Identity users.