Would it be possible to implement a way to blacklist commands not allowed while in parkour mode? For example, I'd like to block the command /pa while players are in parkour because the arena plugin I use (PVPArena) uses that command alias to join arenas.

Despite pa being removed from the plugin.yml as a registered parkour command alias, because it is allowed in the source as a parkour command here d3cbb66#diff-eb8d94763a93fd55979b0adb3e6bc5eaR394, players are able to join the arenas from within parkour with invincibility.

I recommend use PerWorldPlugins. You can get it in here
https ://www.spigotmc.org/resources/perworldplugins.32751/

The condition is now based on command aliases, if the entry is removed from the plugin.yml it will also be blocked whilst on a Course.