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But I take it that if you were to click on a link in one of those windows, your Slack window now becomes... a Gitlab window.

That's a customizable setting in Flow. You can have it launch your default browser or open it internally.

There's also the pros and cons of auth/cookie isolation. You'll need to log in to Slack again. But if you use it for, say, Facebook it will work like the isolation feature in FF.

There used to be something like this built on Firefox. I'm not sure what happened to it.

Maybe you are referring to https://en.wikipedia.org/wiki/Mozilla_Prism

Aren't you referring to Fluid? https://fluidapp.com/