Hi jazzyj,
DXF straight out of PhotoScan should work fin.
Just make sure that you have cleaned any 'untidy' edges of your photogrammetric model. You don't want to generate and export contour lines for such areas.
I would normally generate my DEM (which is needed first to compute contour lines) from the Dense Cloud. You can either classify or delete 'rogue points' (e.g., at edges) in your dense cloud so that you can exclude them during DEM generation. This means you can then generate clean contour lines from the resulting, clean DEM.
Unfortunately it is not possible to clip contour lines in PhotoScan based on digitized shapes/polygons. You could, however, do so using QGIS (free & open source).
All the best.
Regards,
SAV