It would be nice if I could write custom profiles and have that profile extend one of the current profiles.

For example:

If I want some hard bases to have arena walls and other hard bases not to; I could write a new profile called "hard_with_walls.json" (or something) and tell it that it extends the hard profile. In that profile I can then overwrite the arena wall settings and all the other settings will be inherrited.

Taking this a step further, it'd be nice to have custom profiles that extend other custom profiles (as long as there are no cycles obviously, and the top custom profile extends a builtin profile).

This shouldn't be necessary

You're not limited to 5 profiles, nor are you limited to 1 profile per difficulty. You can create as many profiles with as many difficulties as you want and customize them however you want. The plugin will load all profiles in the Profiles folder.

Just create your hard_with_walls profile and put those bases in that profile, using this command (or by doing it manually if you insist):

rb.config add hard_with_walls rbh001 rbh002 rbh003 2

This will create the hard_with_walls profile with the difficulty set to 2 (hard) for you, including additional bases rbh001, rbh002, rbh003 and you can set any settings, including enabling or disabling walls. Replace the filenames with your copypaste filenames.

Reload the plugin and it will then randomly pick between these 2 profiles when spawning hard bases. The only change needed here is if you are using Base Loot tables then you must create a loot table specific to this profile in the Base Loot folder by using the same filename as the profile name, as is the requirement for any profile using Base Loot tables.