I think having a companion drone to begin with in challenge mode makes the early game too trivial
You have to start with one drone because you cannot craft more until much much later in the game. If you're looking to make the game more challenging, this is not the mod for you. "Challenge mode" is not supposed to actually be hard, per se, it's supposed to be "less easy" while giving you a good sense of progression instead of instantly starting with a max power bot.
I’d also love options to make the companion drone slower, have a smaller range, and use more fuel.
Adding in customizeable options like that is not an easy feat unless the mod has been designed with that in mind from the ground up. Speed in particular is very weird and difficult to work with in this mod, because ultimately the companion is a heavily modified Spidertron. You'd think that would make it easier to work with, but somehow modifying the speed in a controlled manner is super difficult. Other stats aren't as finicky, but would still require a lot of tying in to existing methods. Sorry but options to change drone stats is probably not going to happen.
Also, why is there an ‘Enable Challenge Mode’ mode option in the settings in addition to the ‘Set Mode’ setting?
It was a backwards compatibility thing that I forgot to remove in the last update. If I remember right the checkbox doesn't do anything now, it only relies on the Set Mode number.