Carbide burrs are a mainstay in any shop that works with phenolics and epoxy-fiberglass materials. They can be used in high-speed router spindles (overarm type or smaller under-the-table units) for profiling with hand-fed work mounted to templates. Always use them dry with vacuum in that context, especially with fiberglass materials. The actual phenolic grades don't create toxins, unless you seriously overheat them, it's more of a "nuisance dust", to quote the mfr and OSHA data. I spent a fair number of years working around that type of plastic fab. I was glad to get away from it, especially the epoxy-fiberglass stuff. Very annoying.
I'd worry a lot about the end-use product if this is cloth-based phenolic being processed on a waterjet system, as even with the pilot holes, there is still going to be substantial lateral hydraulic pressure driving the liquid into the laminations. Not your problem, I guess.
For the specific hole-drilling application, you've found something that works, so good on ya'. If I were doing that, I might have tried a carbide-tipped twist drill to start, but the big disadvantage you had at the start was the high spindle RPM. I probably would have ended up right where you are, with a burr running at high speed.