Not sure if this is a bug , feature request or missing something in Hekili.

I play two different characters (boomkin and ww monk). For each character I want Toggles set to different values. I have yet to see a way to accomplish this

You can set up multiple profiles via /hekili > Profiles, that will give them their own toggles.

If you copy settings from your existing profile, the displays and other settings will come over from the original profile.