Im tackling this EXACT issue right now but unfortantely Im working on the max side of things...
I have been trying to figure out ways to have it import my mesh without horrible seam screw ups etc and not pre calculating my tangents (Seriously unity wtf man)
I dont suppose you can toss up examples of what you did so I can maybe squeeze that into a max script eventually?
We can talk in pms if you dont wanna clutter this chat.
edit:I also tried chaning up the way the Nmap bakes to keep it Y positive so that unity wouldnt need a flipped Y channel to see if that fixes it , but it still gives me weirdness going on.
Example of what I mean
as you can see on the left side of that box Im having a harsh seam line there as if it has a smoothing group split, but lord and behold everything (but the bottom) has smoothing group 1 assigend to it and smoothing group 2 on the bottom.
And every time I import a .max file or .fbx it keeps setting tangents to "calculate" vs import...seriously I want to smack unity right now this is really hindering progress of the current project I am on!