I've bred bees plenty of times with vanilla Forestry and with Extra Bees machines. It was really interesting the first time, but after that it just became a huge time sink, even with Extra Bees, and I have zero desire to ever do it again. I think, for a lot of us, the convenience of Gendustry (which comes at a cost in energy and materials) is the only way we'll ever bother screwing with the flying pests.
If you find it to 'OP', feel free to not use it, but don't expect a warm reaction to trying to nerf Gendustry for the rest of us.
You're right. I know that I pointed out ages ago to someone else complaining about something being OP or something that they didn't have to use it. I should have thought of that as well.
Given the huge number of bees that are available in general, having something like Gendustry does actually make it possible to breed bees without huge time sinks or the hassle of trying to find the right biome etc.