Like forestry does, when right clicking a water bucket on a machine it fills the tank and return an empty bucket without opening the GUI. If tank is already full, it does open the GUI.
Same goes with an empty bucket to pull the output tank.

Unlikely to be implemented as there is no easy way to get fluid out of input slots.

My suggestion is to:
A- directly add to input tank
B- directly remove from output tank(s).
You're talking about:
C- directly remove from input tank.
I don't think C should be a thing.

To list another mod as an example: ThermalExpansion does the same thing.

Ya but the issue is what happens when you misclick with a bucket?

If the tank is not compatible (invalid liquid type or not enough free space), then it just opens the GUI.
If a player right click a tank with a water bucket but wanted to just open the GUI, then they've learned not to do it again :). It's not like it's new (TE and Forestry already do it), or will trigger a antimatter explosion (Gregtech with water anyone?).