I got tired of not being able to remap the keyboard controls for Star Control that I set it up myself. I'm not sure why this isn't included in the game menu to begin with.
See below for how to add the Keyboard Configuration Utility and Scenario Editor to your game.

Browse to the installation folder. [Manage Installation --> Show Folder]
Select the dosboxSC1_single.conf file. Make two copies.
Rename the copies to dosboxSC1_edit.conf and dosboxSC1_keys.conf.
Edit both conf files in a text editor. Rename starcon.exe to keys.exe in one. Rename starcon.exe to edit.exe in the other.
Configure the executables. [Manage Installation --> Configure]
Select Features --> Custom Executables. Duplicate File 1 twice.
Edit both arguments under the new files. Rename dosboxSC1_single.conf to dosboxSC1_keys.conf in one. Rename dosboxSC1_single.conf to dosboxSC1_edit.conf in the other.
Label them Keyboard Configuration Utility and Scenario Editor.
Select OK.
You should now be able to launch the Keyboard Configuration Utility under Additional Executables.

See screenshots.