Can I fast travel when I would be over-encumbered except not because of a temporary effect?

Yes, drinking a potion that fortifies your carry weight will allow you to fast travel, provided that you do so before the effect expires and the potion's effect is strong enough such that while under its effect you are no longer over-encumbered. I've done this myself numerous times.

A fortify carry weight potion enables fast travel for any distance (as long as the potion's effect gets you beyond the level of being encumbered). The distance/time covered by the travel can be arbitrarily long, even longer than the potion's duration.