As of v0.9.0, Chaudloader has its own GUI for enabling & disabling mods. However, this causes issues with controller players & remote-play (Steam Link), as now instead of autolaunching with the desired mods, Chaudloader pops up an interface with each launch that requires the interaction with a mouse.
As a recommendation, provide users with the option to bypass this GUI with a configuration flag (such as by way of a checkbox), allowing the game to autolaunch, as was previous behaviour, and provide a shortcut or launcher for launching into the GUI directly to accommodate.