Good question. Nobody running the tune has had any issues with respect to the rev limit increase. I haven't had any issues period, except for wanting even more power
The short answer to your question is, from the testing of Visconti's tune to date, the raised rev limit hasn't produced any mechanical issues.
I think you're right generally that increased RPMs = increased wear on an engine as a broad principle, but in terms of specific mechanical issues caused by John's reflash or the rev limit aspect, there haven't been any. For me, the reflash has been perfect and without issue. The flash even smoothed out my rough idle problem, so it's a net positive mechanically as far as I'm concerned.
This is one of John's turbo tunes, however, so I don't know exactly how he deals with the rev limit in the turbo tune.
Belated Edit: John has a kit running 20psi on stock internals with just injectors and a fuel pump, no additional modifications in terms of internals. I think that says something about the durability of our FA20's, and also the tuner and the kit.