Well it's strange, because I've removed config popup in the last update (v 0.3.1).
Unfortunately, I'm not able to support your controller at the moment - but it's on my TODO list and will be fixed in future updates.
Anyway, I did notice the latest update so far, so I installed the latest version and at first it did run.
It ran at 720p windowed with low quality and I again had my gamepad in XInput mode connected. First issue then was how the guy kept moving to the lower right; He did react to moving the d-pad and left stick, but when I let go, he'd keep moving lower right again. Also the buttons didn't seem to be mapped ?(
I did, however, find the pause button and the pause menu showed me the graphics settings which I set to 1080p high quality fullscreen right away; Then I closed the game to reconnect the gamepad and reopened it. But now, with graphics at 1080p HQ full, it keeps crashing on me again everytime I try starting a new game. I tried reopening it several times with and without gamepad and it still crashed upon tryna start a new game.
So I tried to delete and reinstall the game's latest version in hopes it would reset graphics, but it's still at 1080p HQ full and now, for the second issue, I can't for the love of me seem to find the config file that has the graphics settings written in it.
Hey, as I mentioned before - I am currently focusing on developing core game experience and cannot support your controller (but it's on my TODO list and will be done in the future).
Regarding your settings issue: if you are on Windows, you can go and delete all the content from this folder C:\Users\YOUR_USER_NAME\AppData\LocalLow\WolkGames\
If you are on Mac, go to ~/Library/Preferences folder, and delete a file named unity.WolkGames.TurboIslandPurger.plist
It should clear the saved graphic settings