Because I am fairly certain of my proof that it does change the endpoints.
Actually, here let me give an explanation of my smooth isotopy.
Do you remember characteristic foliations?
Take a contact manifold (say R^3) and embed a hypersurface in it (for a 3-manifold, that's a surface, e.g. the x-z plane). Then look at the singular foliation resulting from the intersection of the tangent planes of the surface with the contact field of hyperplanes.
Traces out a singular foliation on the surface
So what I am dealing with here is not just the x-y plane, but the x-z plane embedded in R^3.
It has a characteristic foliation for the usual contact structure of horizontal lines.
Just like our x-y plane example we have been working with
And my smooth isotopy is just a bump function in D, bumping the x-z plane along the y-coordinate.
And this changes the foliation.
And I proved quite explicitly that the leaves do not exit at the same place in t=0 as in t=1.
(if you wanted, I can email you my proof)
But I am fairly certain it's right.
Because otherwise I think contact geometry is bunk because it seems to be implicit that I can do this.
Maybe the fact I am isotoping it in R^3 changes your argument though