We tried make an orthomosaic from multispectral tiffs (70m above ground, forest trees), but Pix4Dmatic makes error at orthomosaic (ORTHO-5 error). It shows green twitch only at half of the pictures.
You may want to try out PIX4Dfields that can create orthomosaics from multispectral imagery. Have you given it a try? It’s usually more thought for “flat” areas like fields, but it may work in your case too. It’s worth a try.
What information are you looking at when mapping the forest?