PSA - or just a bit of useless info:
I have loads of controllers etc connected to my main PC for flight sim flying (and ED of course) - this has resulted in this game interpreting something as a "move left" command continuously and so basically the game controller actually doesn't. I didn't bother trying to eliminate the conflict as the game runs perfect on my laptop and I don't see the point in having to swap out connections as flying is the main use of the PC.
BTW - Why it defaults to Game Controller input I don't know - if there was a way to force it to start in M&K only I'd be happy to try that.
P.S. Still love the game, the humour is great and as a Scot living in exile in Yorkshire I find it very relatable.
I used to have an issue with my hotas being picked up as a primary controller in certain games like FIFA or Assassin's Creed which ended up giving ghost inputs regardless of which control method I selected in game, usually found the main culprit to be the hotas throttle unit, having the most switches, knobs and buttons on it...
Solved the problem by plugging the hotas (and other peripherals) into an external 11 port, powered USB hub. It has individually on/off powered USB-3 ports so I can turn off whatever I'm not using via the power button on each port...saves crawling around under my desk pulling USB plugs out of the back of my PC when I don't need it.
Although I've got more than enough (10) USB ports on the IO panel on the back of the PC plus a further 3 USB-3 and a USB-C fast charging port on the front panel, the only USB peripherals I've got plugged in to my PC directly are my mouse, keyboard, the USB hub itself and my Tobii eye tracker...everything else is plugged into the hub except for my Xbox Elite V2 and Nacom 5 Pro controllers which are both Bluetooth.
Definitely worth a look at a powered USB hub if you have a few peripherals like wireless headphone dongles or charging cables, Xbox controllers, USB flash drives, portable USB storage drives, hotas etc, they're only a tenner or so from Amazon. There's certainly no introduced input lag by plugging peripherals into the hub versus directly into the IO port or anything.
On the hub I have, the 3 ports on the left (red ones), plus the one in the left hand end of the hub with my grey phone charging cable in it are 12v power only, the other 7 (blue ones) are normal data/power USB-3... cost me £11.95 from Amazon a couple of years ago. Fixed it to the desk with some 3M double sided tape to stop it moving around although it has 2 screw holes in the bottom of it for wall mounting etc. The ports light up when powered on, stay unlit when powered off. Overall, it's the most versatile (and cheapest) PC peripheral I've ever bought