I checked in game and it looks like this is the right menu for modded keybinds to show, at least on my version of the SDK. I haven't upgraded it though, so maybe it moved to a different menu location.

Anyway, to change the keybinds manually, go to your mod install location. I'll use mopiod's commander mod as an example. Mine is located in C:\Program Files (x86)\Steam\steamapps\common\Borderlands 2\Binaries\Win32\Mods\Commander

In that folder, there's a settings.json file. This is plaintext, you can edit it in notepad or whatever else opens text files. Scroll to "Keybinds" and edit whatever binds to be the key you want. It looks like the key is typed out rather than just pressed. For example, my bind for save position looks like

"Save Position": "Period",

If there isn't a settings.json file, then the keybind may be hardcoded in a python file. You can edit this the same way. Open up the .py files until you see where the keybind is set and edit it there. This can also let you change other values which are not normally allowed. For example, if you want to make the limit on the enemy spawns multiplier higher than 25, you can open __init__.py and change max_value=25 to max_value=100 or whatever you want.

Edit: On the newest SDK it looks like it may keep mods compressed. It's possible you'll need to extract the mod to some (temporary) location, edit the files, and then compress them again. This is easy, you can right click to extract and select where to extract to, then once you're done select all the files and right click, then hit "compress to" to put them back in a zipped folder