Commands cannot be disabled or swapped out directly, no.
You could go about this a number of ways:
Put all the logic in the same set of commands, using conditions to choose which branch is executed, depending on the vehicle/weapon you're using
Use different commands for each vehicle/weapon, and use a single command that is activated by a button press which again contains branching conditions, this time to choose which command is executed
Rather than duplicating commands between profiles, use one profile for each vehicle/weapon set, and one common profile containing the "agnostic" commands which is then included in the vehicle/weapon profiles.