For those wanting to play this game with a controller, but didn't want to deal with only having keyboard prompts, I was finally able to make a mod to mostly fix this issue. See the links below for where to download the Controller Prompts Mod.

Nexus Mods:
https://www.nexusmods.com/relayeradvanced/mods/1

Game Banana:
https://gamebanana.com/mods/490768

And here's the link to the game's PC Gaming Wiki page:
https://www.pcgamingwiki.com/wiki/Relayer_Advanced#Controller_Prompts_Mod