Yes, we are working on integrated debugging technology (what our customers mostly do these days is just run a conventional debugger inside the simulation, but that doesn't quite use our full power).

You're correct that tiny things like modifying the binary under test or attaching a debugger can change determinism and result in the bug slipping away. That's why... it's a good thing we've already built autonomous bug-searching technology? Since a deterministic hypervisor is also a hypervisor, we can generally rewind and do the intrusive debugging action at the "last possible moment", when it's least likely to cause the bug to disappear. Then if it still does, we simply fuzz onwards from that point and re-find the bug. This usually goes pretty quickly because we're in a timeline that's "close" to it, and we can use clues from the original repro to guide the fuzzing.