Glad you like it!

1. You could configure Left Clicks (Global or per Website) to open in a new Temporary Container - that way they get focus.

2. In a future version there will be a way to activate "Isolation" (Global and per Website) which will open *all* Tabs and Links opened by Tabs in a new Temporary Container - even when opened programmatically; and that's what's happening with Foxy Gestures. With that feature you could achieve opening Links with gestures in new Temporary Containers. Another way would be to get in touch with the Foxy Gestures developer and ask him if he'd be willing to implement an API for other WebExtensions that allows to register to events inside the Foxy Gestures WebExtensions (that way I could get the information that the tab was opened by Foxy Gestures).

If that doesn't help, you need further assistance with configuring or you got some Feedback from the Foxy Gestures Developer then please open an Issue on GitHub (https://github.com/stoically/firefox-add-on-temporary-containers/issues).

Edit (18. Feb 2018):
Support for Foxy Gestures User Scripts are now available, you can find them here: https://github.com/stoically/firefox-add-on-temporary-containers/wiki/Foxy-Gestures-User-Scripts

Edit (6. Mar 2018):
The "Isolation" feature is now available