you can do normal rjs with a ctap script
you can use a crouch+jump script and a ctap script at the same time
you can do all 3 things with both scripts on perfectly fine
the only thing you can't do normally are those particular bounces on jump maps where you get the precise height you need to bounce by doing an uncrouched, you'd need another jump bind like scroll wheel or something, or those jumps where you do syncs by going through sequential teleports by jumping into them, doing a crouch jump makes you take them 2 at a time
there's also the funny where you can set up a script such that pressing ctrl modifies your jump key so you do a normal uncrouched jump, making it so spacebar alone gives you a crouch jump and doing the normal 2 button input to crouch jump gives you a normal jump in the rare situations you want it.
of course that generates a new problem where ctrl doesn't make you crouch anymore