Bit of a 'blood bath' but that looks a useful mod. Gives good access into the rear for tools. Was the access between the seats before?
I have a crew cab hilux (4 door) that the rear seats fold up into the rear of the cab giving an open storage area. Nobody has sat on the rear seats. Only ever used for tools and materials.
Are you fitting the window in the door to match the offside?
The side doors can have a buffer fitted to the wing to prevent damage as the doors fold right back against the body.
If you shorten the rear door this buffer would need to be on the passenger door. May need that area strengthening/supporting to avoid a dent.
I am not sure if a door stay is available for the standard side access doors.