Title Pretty much explains the question, would it be okay to do this when the engine is hot. the gearbox would also be hot obviously.
It's sort of like an oil change after driving around a bit. The only real concern is burning yourself.
Of course, this being the transmission, you are less likely to burn yourself because "hot" for a manual transmission isn't really that hot. The oil is subjected to extremely high pressures (between gear teeth) but nothing that's combusting.
Just remember to always remove the fill port bolt before the drain plug if you decide to drain and refill. I do also wonder why you need to "top up" MTF... It's normally a sealed system.