I'm a felt fan. I've never had rubber that came anywhere near felt on slimy stream rocks, but I've had rubber that is a fair bit worse.
As far as longevity, typically the boot wears out before my felt does.
I do agree felt is inferior on mud and snow. Both are fairly rare for me to encounter while trout fishing.
That said, yes, I do certainly think it's possible for felt to transfer invasives. I have 2 pairs of felt to rotate, and lately my fishing has been more quality than quantity. If a single pair of boots sees two different streams within about a month of each other, I do the clorox thing in between. That hasn't happened since July. Return trips to the same stream, and boot rotation when I don't, have kept me from having to do it too often.
The easier answer for me is freezing. It kills didymo and is easier, better for the boots than a clorox soak. But it's didymo specific, it may not prevent transfer of other things. And while easy, I'm not sure my wife will approve of wading boots in the freezer!