Removing all files doesn't clear all inputs in the GUI
After removing all input files you wonder why some of the other settings still contain information. You want to start with pristine settings.
This is intentional behavior. The functionality "remove input files" is not supposed to revert the setting into a pristine state. The tool tip in the preferences hints at this. It only removes the input files, the tracks, and it clears the output file name and the file/segment title if and only if those two have been set automatically (enabled in the preferences). The other controls (e.g. split settings, chapters, attachments…) aren't touched.
This behavior allows users to multiplex several files sharing common settings in succession quickly.
If you want pristine settings right now, just select "New" from the "Multiplexer" menu.
If your use case is to start over with pristine settings after multiplexing, then set the option "Clearing settings automatically" on the "Multiplexer" page in the preferences to "Create new settings" — that's what the option is there for.
You can even chose what to do with the settings each time you start multiplexing by pressing on the little arrow next to the "Start multiplexing" button. It'll show a popup menu with options what to do directly afterwards, e.g. open new settings. This overrides whatever's set in the preferences.