Thank for your inputs and maybe I should have added that the Swiss Coordinates CH1903/LV03 (EPSG::21781) are a projected coordinate system (and WGS84 a geographic coordinate system). Therefore one need to re-project the coordinates and therefore choose an ellipsoïd for the vertical correction.

In this case, I dunno if Agisoft chose the WGS 1984 Geoïd, the current Swiss Geoïd CHGeo2004, or a European one?

I'd like to know which one and what are the resulting elevation (Orthometric height, Ellipsoïd, Geoïd?)

Any thoughts?