Is there a way I can isolate the VIP livery from using the same config as the Air Canada one? For example, the cargo doors are used by GSX for my Air Canada flights but I don't plan on using them with the VIP version.
Not possible at the moment. The configuration is tied to the Airplane folder name, which means you could achieve that by putting that repaint in its own airplane folder, but I don't advise doing that.
We'll note this as a suggestion for a future update.
Second question: Is there a way to configure airport parking positions? I know there is the editor for all that relate to the trucks' positions but I really mean the parking positions.
That information is taken from the scenery AFCAD. There are several good AFCAD editors out there like ADE or AFX that allow changing anything in the airport parking and taxi layout structure, it would be a waste of time duplicate that features.
Third question is if there is a way to edit the path the trucks will use... For example, when I fly into Santiago (SCEL) the trucks upon leaving the aircraft area with the luggages will go straight into the terminal building instead of taking the roads to get there.
Same as above. GSX will use vehicles taxiways by preference, if they are available. This means, you can probably fix this by adding more taxiways of the Vehicle type in ADE/AFX.