So are you saying that there's 2.5mm height between the end of the fretboard and the strings when the bridge is at its lowest position? This may be fine for you and the way you have your basses set up, but if you feel you want a lower action, then there's currently nowhere to go. When finished, with the strings up to tension and some neck relief set, this distance may increase slightly. Also, I don't know anything about that bridge, but if it's at its lowest setting, is there a good break angle for the strings over the saddles?

I once had a custom made super-Strat with a Kahler trem. I had to get the trem inset in the body by a couple of mm to get a decent string break angle over the saddles before it started playing and sounding really good (changing the neck pitch would have caused too many problems with pickup heights as they were directly screwed into the body).

I'd just check as well as you can that everything is OK in these areas before carrying on.