As far as I know, no unfortunately. I've also tried it. Tuneboy files are .dat if I recall correctly, TuneECU are .hex.
If you think TuneECU support is scarce, Tuneboy is worse ime. I think TuneECU support is greatly misunderstood by the masses, they're always asking basic questions which are answered in the FAQ or questions about tuning rather than the tool itself if you get me - as if downloading the software comes with a 24 hour hotline to a tuner. And as such don't get responses from the TuneECU reps. Perhaps that's where the customer support rep comes from.
Unless someone out there has a TuneECU map for the supercharged engine - you could manually copy table values over from the Tuneboy map to create the TuneECU version. Tedious job but this is what I did for the Carpenter 240 map.
Or you could load a "stock" TuneECU map and a local tuner can tune the bike with trims in PCV and ignition module, then import the trims into the TuneECU map creating a custom TuneECU map for the supercharged engine.
Another option is find a tuner who will work with TuneECU and pay them millions to develop the TuneECU map with your supercharged bike.