The limits of tools only expose themselves when they're being stretched in ways the authors did not intend. Good tools have enough escape hatches to get you by those moments, and the bad ones break down entirely.
Such tools should have a degree of "hooks" built in so that work-arounds are easier. For example, a ORM should have an operation to send direct SQL to the database for the times it can't generate SQL as intended. And maybe even modify specific clauses if needed so it's not all native or all raw, but something in between. Of course, if it's too open-ended it becomes a hacker's playground, so a happy medium needs to be found.