Update: I've got it to work! Here's what I did.
1) Went to the Launcher app, then "additional settings in the app," toggled "Add app icons to home screen" on and off. (This was already on, all I did was turn it off then on again.)
2) Force stopped Vanadium (which I had already tried before).
And that's it. Right after these two steps I went on to crypt.ee and the "Install app" option was there.
One more note to make: crypt.ee does not appear in a custom launcher that I run. It only appears when I'm running the native Graphene OS launcher. After the two steps above, I do have the option to install crypt.ee when the custom launcher is enabled -- I just don't see it anywhere after it's installed.