Most effective software for creating orthos over water?

I understand that water can be a very challenging environment to work with due to glare, wave action, and refraction. Im looking for any personal experiences of people who have successfully made some orthophotos over water to effectively map the bottom of said water body (given its shallow and clear enough).

I ask this because I am presented with an opportunity to create a large scale orthomosaic of shallow water coral reefs as part of an undergrad research project. Im working with an Air 3S, so survey grade accuracy is not really needed because the Air 3S doesn't have RTK-GPS or SDK support anyway.

I've used WaypointMap in addition to AerialModel and Pixpro so far to generate some test orthos of salt marshes near where i live. Pixpro does NOT like water at all, but ive actually had decent results with AerialModel despite some noticable stitching issues here and there. Based on the results, I suspect that AerialModel doesn't generate a point cloud to make the ortho, but rather just stitches the images together in the same way a panorama does.

Some research articles I've read seem to like Agisoft Metashape. It seems to work well, given you plan accordingly to reduce glare and whatnot. I would just like to avoid spending that kind of money considering i don't have a survey grade drone, I will if i need to though because I i do plan to get one at some point.

Anybody have first hand experience with something similar?