Think Bodnar are just covering themselves as they would rather people didn't do mods directly on the boards. Having said that building joysticks and cockpits is all about doing modifications, so with a little care there should be no problem.
Have to say the Leo Bodnar range of boards are excellent, and at least if you do brick the board, it's not too expensive to replace!
Have just used their BU0836A board on my recent full size 1920s joystick construction and it works beautifully.