No matter which default units I choose in Photoshop settings, the free transform units are always set to percentage when the application start.
I can then change them to something else (e.g. pixels), but they're always back to percent the next time I start PS.
It doesn't look like there's a way to set a default unit for this particular, and while it's not the end of the world, it's quite annoying and it would be nice too see it fixed in the next (minor) update.