Photoscan is displaying linear 16Bit TIFFs in an sRGB colorspace, causing the viewport and photos pane to display the photos inaccurately - with much more contrast than expected. It would be necessary for a linear workflow to have support for a 'working colorspace' where the user can set Agisoft's working colorspace.
Out of curiosity, is Agisoft performing reconstruction on these linear images in sRGB space?