okay, if you choose to ever want to use the A2A Configurator, for instance to easily map gear and flaps levers of the P-40, you can 'enable' all the controllers in FSX without it interfering with anything related to FSUIPC (or Linda, I surmise), even going so far as to remove every last button/keyboard/axis assignment within FSX. The controllers are still 'enabled' they just aren't being used for anything other than what you choose to do within FSX, and that might be nothing. There shouldn't be any any problem customizing controls, nor need to change settings for each different aircraft in any case.
I use controllers enabled in FSX (just not anything mapped in it like buttons or axis). I use the A2A configurators for the ease of programming the most used functions and I supplement that with LINDA and FSUIPC.
This causes no issues to me as long as I don't so something stupid like duplicate a control.
So it is possible to enable the controls in FSX to use the excellent A2A configurators without it causing issues to other control input methods.
I have run into situations where having both FSUIPC and FSX trying to control axises will cause fluttering of the control surfaces, as FSX and FSUIPC fight each other over the controls. If I recall correctly, Peter states in the FSUIPC manual that if you use FSUIPC to handle the controls, turn off (disable) the FSX controller.
I don't know how this affects buttons? However, by using the "Specific Aircraft" feature in FSUIPC, I can set the controls once and then forget about them. FSUIPC will recognize the P-40 and change the global settings to match the P-40. Afterward they will be reset to global. If I change the button for the P-40 in FSX, I have to change it back afterward to what it was globally.
An example of this is the 'Drop Weapons' button found on the Warthog and other combat sticks. I use it to fire missiles and drop bombs in aircraft that allow that. This is the perfect button for the hydraulic pump in the P-40. If I can get it to handle the hydraulic pump in the P-40 through FSUIPC, it will function this way only in the P-40. Another is the Master Avionics/Battery. Some developers use the master avionics to control the electrical system. Others may use the battery function. With FSUIPC I can set each command to a single switch. FSUIPC will recognize the airplane and set the function as needed, without any input from me.