No, there is no reason not to do it. The switch manually simulates exactly what the temperature relay does, so the motorcycle's electronics cannot discern the difference.
as for your questions:
Will it have an affect on the motronic? No, the Motronic is totally out of the picture. The fan is controlled only by the temp relay.
Or if the engine gets hot enough to signal the fan to come on, and you have it on already, could that be an issue? No, not an issue. The switch is wired either to simulate a severely overheated engine, signalling to the relay to engage the fan. Or it is wired to parallel the relay's contacts and supply power to the fan. In the first case, the actual water temperature will never get "hotter" than what the switch simulates. In the second case, if the relay tries to turn the fan on, the switch contacts parallel the relay contacts and nothing untoward happens.
I am just curious because the popular spot to connect a manual fan switch seems to be at the temperature switching unit. There must be a reason for that? Yes, because the temp relay is the brains behind all control of the fan.
