Sequential would not like my mixing of tracks I guess
Mine neither. But that is not the reason I do not use it.
To reiterate
...it will not match adjacent images in parallel runs
is the reason.
Sequential works well with planned mission drone flights. We divers are not drones. Its not going to fix your issue, but if you want to try it then I believe its based on the EXIF image creation time, not filename or folder structure.
Each camera image should align to its neighbour. But no alignment will occur between the camera image sets using sequential. A second alignment will be needed with Reset Alignment ticked off to align all points.
And to reiterate:
Unless the GPS data is accurate then adding it won't help.
If you really want to go the accurate underwater GPS route then its possible. A budget minimum of perhaps $70~100k would see the issue fixed, but it will still come with limitations, setup and working methodology that would add time to the work on site.
Remember, everything can be fixed...but it all comes with cost.
If you have not used video then don''t bother - stills will deliver more data for less work.
You may be generating more images and therefore more data than is required to produce a result. The entire Thistlegorm - 7 acres - took 24,000 DSLR images (see
https://deep3d.co.uk/2020/05/03/the-ss-thistlegorm-content/. More images is not always best...its the correct number we really need.
Shooting at 3 to 4m from the subject should provide massive coverage...thats far too distant for my style which is typically 1~2m to allow the strobe light to restore colour...my gut feeling is there are more images than really needed in the project.
There is no magic silver plated solution here.
There is a mass of data to work through, You could spend more on processing hardware, change the cameras...but the basic approach of how the images are captured might be the best place to start - and its zero cost beyond the time needed.