Hi obw,
I don' think that it is necessary to work with full resolution imagery to create your 'timelapse' video. Even for a 4K video, the resolution of each individual frame is only 3,840 x 2,160 pixel (about 8 Megapixel).
Therefore, it is sufficient to export 8MP orthomosaics from Photoscan. But make sure to always export the exactly same area (probably best to use an OUTER BOUNDARY). Then save all orthomosaics as jpgs and import them into a video editing software (e.g., Adobe Premiere, iMovie, Windows Movie Maker,...), add a smooth transition between all of them, render and export the video. DONE.
Regards,
SAV