If these apps have on prem, or some other technique for customizing the domain, the extension could request optional permissions programmatically in response to engaging with the extension icon.

I think they'd be good additions. <all_urls> permission leads to extra review scrutiny when submitting a build to the Chrome Web Store. And if you get popular enough there will be gentleman callers that want to buy your extension (and your users (to run custom js of unknown motive on all their websites)).