I believe primarily to assist with gamepads and devices with limited input, Chocolate allows remapping of all keys in all the games, including an added previous/next weapon switch.
For Doom, only the keys displayed in the primary menu of chocolate-doom-setup are remappable in vanilla setup.exe and saved in default.cfg.
In Heretic, Hexen, and Strife, all of them have more remappable actions in vanilla listed under "More Controls", with the rest under "Other keys". In all games including Doom, the weapon selection keys are listed under the "More Controls" category, which might have the possibility of categorizing them as keys remappable under vanilla, giving an unexpected surprise if the default/heretic/hexen/strife.cfg is copied over to a vanilla directory.
It seems to me that the two should be separated, Doom shouldn't have a "More Controls" option and instead, all of the weapon binds should be moved to "Other Keys". Perhaps over the top, but maybe somehow make it clear that you are violating vanilla behavior somewhat by remapping them.