For those of you who can't see the mod settings:

As others have said, certain mods cause them not to appear, I'm not sure of all of them but for me the issue came from random plus.

Here is a step-by-step temporary solution until this is fixed by the mod authors (if it ever is):

1) If you know the mod causing it, temporarily remove that from your active mods list, if you don't know, temporarily remove all but this mod and any dependencies/mod options mods.

2) Start RimWorld and the mod options will appear, make your changes and exit the game.

3) Add the conflicting mod, or all of your mods, back to your active list and start the game. You may see a red error regarding the settings menu for the mod but the options you chose will be in effect and as far as I can tell, the error is harmless.

4) (optional) If you ever need to clean install RimWorld, you might know to clear the folder that mod settings are saved to, here we can make a back up for this mod's settings so we don't have to do steps 1-3 again afterwards. The folder is located here:

C:\Users\(Your profile name)\AppData\LocalLow\Ludeon Studios\RimWorld by Ludeon Studios\Config

Google how to show hidden folders on your OS if AppData isn't there. Might also be a different path on Mac/Linux.

Inside this folder you will find an XML file called: Mod_2854967442_SkillsMod.xml or something similar. The main part of the name that matters is "SkillsMod". This is the settings file for Vanilla Skills Expanded, simply make a copy and put it somewhere else on your computer. If you ever clean install and wipe your RimWorld appdata folder, remember to put this file back in a folder called Config inside the "RimWorld by Ludeon Studios" folder afterwards.

You can create these folders yourself if they aren't there when you do this step. Just make sure they are spelled correctly, structured, and capitalized exactly like you see in my file path above.

DISCLAIMER:
IF THIS MOD IS UPDATED, THE BACKUP YOU MADE IN STEP 4 MAY OR MAY NOT BREAK, JUST DO STEPS 1-3 AGAIN.