You are correct about point controls overriding constraints, but which control overrides which constraint is dependent on the types of constraints. For instance, if you have a Slope and Horizontal constraint on a point, and you apply a Horizontal control, then the Horizontal constraint will be replaced by the Horizontal control, but if you have a Slope and Vertical constraint, then the Slope constraint will be replaced with the Horizontal control.
Also, when a Superelevation control is placed, there is an additional check for recursion on the pivot point, and one or more constraints may be removed from the pivot point if the pivot point is being controlled by the superelevated point. This will sometimes give you strange results like the one you are seeing.
Sounds like your point constraints ( Vector Offset) within the template may be causing unexpected behavior. One way to test is to free some constraints in the Create Template command and move the points in and out and up and down to see if this may be causing the problem.
If you run into problems and cannot debug this issue, let us know and we can take a look at your data.
HTH
Thomas