> We understood that the new Xcode signing was designed to allow such use, but Apple has indicated that this should not continue.
Where has Apple ever indicated that the new Xcode signing was intended for your use-case? I never saw the download you provided, but I'm assuming you didn't actually release f.lux as open source, but instead just provided essentially a prebuilt download and had Xcode re-sign it. Is that assumption correct? Because that seems to be a pretty blatant violation of the spirit of the developer program, even if it's not explicitly spelled out in the agreement. The new Xcode signing model is intended to allow people to get started with iOS development without paying any money, so they can build and run their own projects on their own devices, and only have to pay for the dev program when they want to start distributing to other people. If you did in fact release f.lux as an open-source project, that would be within both the spirit and the letter of the agreement (I doubt Apple has any problems with people installing open-source apps on their personal devices). But it should be obvious that Apple wants all binary distribution to be done through the app store (or enterprise distribution where applicable).
Speaking of enterprise distribution, did you ever investigate that approach? I'm going to guess Apple has some stricter requirements on getting an enterprise developer program account, and I don't know if there's any restrictions in the agreement. But I've never actually looked into it myself so I don't know.