You'll want to setup F4SE_loader as a tool, (though it should do that automatically, least it did for me) in the screenshot I post you'll see add tool on the bottom right. Click that and browse to the F4SE_Loader.exe. If you are lucky, you should see it already in the list like mine (it's orange highlighted one in the screen shot). If it's in the list, you can click on the 3 little dots and then select 'Make Primary' and the when you launch Fallout 4 it will always start it through F4se_Loader.exe. To answer your question, if F4se is launched through Vortex, yes mods will work. If you are launching from the actual Fallout 4 folder, then no they wont.
