To be honest, this is off-topic. If you know how they go about collecting fees, please elaborate.
My solution for that is, do not use it.
This isn't a solution, it's more like avoiding the problem, people use custom firmware for a reason, nobody is willing to go through the process of installing custom firmware and pay fees on top of that for the sake of having fun, the stock firmware sucks big time, custom firmware can even fix some miners which is one of the main reasons why I use it, many hash boards report dead on the stock and work just fine with custom firmware, people spend thousands of dollars on these gears, when a custom firmware can fix their broken miner or/and give them the ability to tune it as they wish, they will use it, it's common sense.
If someone want a change, compile your own version, all Information are out there in the wild, you only need the will to do it (don't be lazy).
You are right, but..not everyone has the skills and time to do that, I have not looked into it (probably won't) but the fact that there are only 2-3 major custom firmware out there makes me think that it isn't easy to do because if it was - we would see a thousand different versions and their fees would be a fraction of the large 2% or 4%.
The solution is rather simple, Bitmain makes a proper firmware or we start a fundraise for someone to improve the obsolete Cgminer code, I will be the first to donate.
Until that happens, many people will be "forced" to use custom firmware, I do avoid custom firmware as much as I can, but sometimes you gotta do what you gotta do.