Phenomena like DIBL will lower the effective VT of
FETs in absolute terms. None of the lengths you show
are likely to see much of this in submicron technologies.
Edge effects may also be a factor, a small region at the
edge is a somewhat effective MOS structure but with some
degraded attributes from strain and oxide / interface
quality. The wider (with W/L) you get, the smaller a part
of the composite device's conduction has to do with that.
Delta-W from lithography may be positive or negative.
Now you have to distinguish between what happens in
the simulator, and reality. Some of the numbers seem
like "who cares?" kind of small differences, and the more
"interesting" behavior lies to the left of charted values.
It would not surprise me if all this were simply fitting
artifacts.
I would blithely ignore a millivolt VT difference since I'm
used to seeing 5mV-range mismatch on identical ones.