Dumping heat is a bit of a misnomer to be honest as the air coming through a rad isn't exactly hot. Warm yes, and in closed quarters with a lot of components it can contribute to higher temps.
But ultimately the AIO water is just part of your overall air flow, so orient the fan whichever way makes sense. If you're running intake fans at the front then it makes sense to have the AIO running as an exhaust just like any rear case fan would do anyway. If you have roof-mounted exhausts then you have no issue running an AIO water as an intake because warm air will just get sucked up and blown out the top straight away.
On Mini ITX cases, for instance the Sugo SG05, you have a big fan at the front as an intake anyway, and that's how you'd have the AIO water set up (as I've done on my SG05) and then have airflow over the motherboard.
Ultimately though, air coming off a rad or a heatsink is never "hot" and won't adversely affect cooling performance of an overall system; bad airflow is more of an issue than free flowing warm air.