Hello tuffi,
The tie points that have projections on the masked area can be invalidated using Python scripting. Also it can be scripted to select and invalidate the tie point based on their color. Additionally you can try to select them using Gradual selection instruments, as such points may have higher reprojection error and higher uncertainty value.
But masked areas will not be considered for the depth maps ant texture generation operations, so if you are not planning to optimize the alignment, it may be not reasonable to remove the tie points.