jbexx said:
Only the X and Z basis vectors are specified, the Y vector is calculated using cross product, so I think all snaps follow the same convention.

You're right.
Too bad. Then the reason is something else.

jbexx said:
The matrix between the 2 snap points is written directly to the object, and isn…

It's not possible to prevent flipping if you construct a tangent for given normal, but if your tangent is free, you can minimize it's change over time with a changing normal. To do this, you need to store the tangent (or the whole matrix), and keep rotating it each frame so one chosen axis matches …