That sounds like one of those things where only option is to comment about it to paizo until they decide to change how license works. Though I dunno how big 2e 3rd party customer base is so dunno how much noise could be made about the subjectI have to agree with this. I pioneered the "scratch-off the serial numbers" method with the Book of the River Nations that other Pathfinder compatible publishers used, but there was so much more we couldn't do that we wanted to do. We wanted to make side quest adventures, details about specific locations, etc. None of that happened because we felt that the amount we'd have to scratch out to make it generic enough to work license-wise would make it so generic that no one would know what we were referencing. Ultimately, we did monsters, assassins, and rules reprinting with our own additions.
Players and GMs don't want to switch away from a setting they know and love. So its a choice between generic setting (which is BORING) or making my own and trying to convince people to switch to your less supported setting (which is frustrating).
I love publishing for Traveller. Know why (besides working in a setting I personally enjoy)? Because I don't have to convince anyone to play my stuff. GM's know it is for the setting they already know. From there, it's just a matter of demonstrating the quality of our products. Do I hate the fact that I am (essentially) paying for the license as opposed to a free license, that I can only sell at DriveThruRPG, that (other annoying stuff about the license), yes. But I will GLADLY take them over making more genericness any day.
While I don't publish DMSGuild, we did consider it. Very much so. I think our number of 5e releases reflects our enthusiasm for the generic.