Is it a new Spirit 6 of current production (China)? I purchased one last year and noticed the same problem you cannot get a proper low action, at least the one I ma used with my main guitars. I also lowered all saddles all the way down and still the action was a bit high for me. After lowering the saddles string buzz came out, then had to fret level the fretboard (I am luthier partime as second hobby/job, did luthier training). After fret leveling it became playable because of the fret leveling, still the action not ideal. As Be.eM says one should remove the trem and route the base on the body. Did not do it as I sold the Spirit to a friend that liked the action as it was. As I like Steinbergers, after some research I have acquired three more used ones, two of them are the Synapse SS-2F made in Korea, these are of outstanding quality and can get very low action, also the fretboards are flawless. The third Steinberger, just got it, is a made in USA GU 7R Custom, hand made by mr. Steinberger himself for someone as there is his signature on the back of the body. This one, after all these years is a killer instrument all perfect. Action at 14th fret 1,50mm at low E-string and 1,25mm at high e-string. That is how I setup mall my Ibanez and strats. Same setup for the two Synapse SS-2F. I suggest yu fine a used made in Korea Steinberger these are very good.
By the way here is the best setup I managed to do with that Spirit 6 strings (made in China):
Neck relief: 0.10"
String action at 12" fret from Low-E to high-e: : 4/64" all strings
Pickup height, all pickups: 2,0mm at low-Estring and 1,5mm at high e-string
I always measure the string action at first fret and write it down for all guitars I build o setup/repair. (in this case it is a zero fret):
E: .020"
A: .020"
D .023"
G: .022"
B: .020"
e: .015"