I'm not sure why you appear to be having unique issues that no one else seems to be having.
"The Big One" in particular is absolutely not normal behavior and that works perfectly fine on my machine, and likely also works on the other nine thousand downloads. And I have played extensively both with and without challenge mode. I use this mod in my own regular playthroughs. It should automatically return to the player to dump its inventory when it starts getting full. If it is not, then you have a bug. Have you tried disabling all other mods to check for conflicts?
As for adding 4 roboports... how about you just don't? If doing so adds an "obscene" number of contacts and range, then you don't NEED four roboports--1 is already fairly powerful and 2 or 3 should be more than enough. Try adjusting your behavior instead of proceeding with old-version assumptions and thinking the mod is wrong because now it behaves differently.
Oh and on challenge mode being useless... If you loaded a save, watched the bot for five minutes, then wrote it off, then yeah it seems pathetic. This is by design. It's supposed to be kinda crappy when you first start, because you literally just wrecked your ship--you're lucky the drone still even works. But I made the bot upgrade very soon and very fast because of this. Just research a few technologies and it should be much better very soon. For example, researching electronics will double its default travel speed, and then researching automobilism will nearly double it again. If you didn't want it to start out slow and crappy, then don't enable the mode that makes it start out slow and crappy ¯\_(ツ)_/¯
Finally, the two toggles, that's just something I forgot about and never bothered fixing. The checkbox does nothing. The number controls everything.