To reproduce the subdomains issue I'd need some steps to reproduce (ideally in an GitHub issue: https://github.com/stoically/temporary-containers/issues). Most of the time the issue comes from the fact that other domains are in-between when the redirect happens, which then causes the isolation.

"Open in New Container Tab" in combination with MAC isolation not working is expected behavior since the isolation will overwrite it (See: https://github.com/stoically/temporary-containers/issues/170). Alternatives to disabling the Add-on is globally toggling isolation, using the Alt+i shortcut (needs to be enabled in the advanced preferences under "Keyboard shortcuts") or the "crossed circle icon" in the toolbar popup (needs to be enabled in the general preferences).