Theme color is now set in the Icons & Logos page which is fine if you are running one theme. 

If you run multiple themes with different colour options, you have to manually edit the includeMeta template.

Would make more sense if the theme color was set within the themes options. 

The theme color is used in the manifest file, which is a single file that is theme-independent. Subsequently, you can only set one color for your "theme color" I'm afraid (and it's worth noting this color isn't really used anywhere within the suite, it's something user agents can make use of when supporting PWAs).

It’s also used by Chrome on Android phones to change the colour of the browser UI at the top to match your site.

So if I have a one Red theme, one Blue theme and one Green theme, I’m unable to change the Theme Colour to match without editing the includeMeta template.

 

Yes, however the manifest file is fetched separately (indeed, with Chrome in my tests, it doesn't even use your normal session - it's fetched separately as if a guest fetched the file). That is to say, it is not reloaded on every page load and thus isn't going to inherit your current theme's color regardless. You would actually need to go into your device options and clear your site data for your site in order to force your phone to refetch the file (or wait for whenever it decides to periodically check for updates).

The "theme color" option in a manifest file just doesn't work in the manner you're thinking I'm afraid.