Aaah, yeah, it makes more sense now!
In my opinion, the higher tier modules makes up for the beacon overloads, but it is indeed subject to interpretation, I've noticed a lot of people don't bother doing modules 4+
For the options, it's pretty easy, there's 3 parts. 1 : defining the options in the "settings.lua", you can easily duplicate the innermost { } and separate them with a comma, change the name and maybe the default_value, using "bool_settings" is the easiest.
2: Setting the text, in the locale file, simply set it targeting the same name under [mod-setting-name].
*Note that you can also put a description (hover text) if you set some text for the same name, but under [mod-setting-description]
3: And finally, wherever you apply changes, you can querry your new setting first, just copy the noble-se-tweaks-bettermk3 usage and change the name.
I happens to be a game dev by trade, so I modified the mod to my liking and gave it to my co-players, but I quite like most of the tweaks you add, so I'd love to be able to simply update for any of your future good ideas!