My guess is that the cv boots near the transmission had a little bit of grease seeping out of them, which is pretty common. On some turbo subies, the passenger side boot will fail and split open due to the heat from the exhaust system. Since the dealer replaced both front axles, I don't think the boot split. You'll know if the boot split because even after being cleaned up, you will still probably be able to see cv joint grease residue sprayed in some places. At 60k, I'm guessing they could've just put new clamps on the cv boot and you would've been just fine. I highly doubt that it was necessary to replace both half shafts.
Aftermarket cv axles only seem to be a problem with automatic transmission subarus. With aftermarket cv axles in automatic transmission subarus, you may experience a vibration when at a stop with the transmission in drive, but the vibration typically goes away if you shift to neutral. Manual transmission subarus do just fine with aftermarket cv axles.
*One more quick note. After the axles have been removed, it increases the chances that transmission fluid will leak out past the axle seals, since the axle seals are somewhat delicate. So just something keep an eye on as well, since the axle seals are annoying to replace.