So, i've tried to replicate the situation and stumbled across some issues.
Since the original dataset was too large I just ran several alignments on a subset of the imagery in the area where larger errors occured. Interestingly enough, suddenly I was not able to align all the images using the "generic" option.
Attached are some screenshots, the original "generic" alignment was done with a version before 1.2. Here one can see the error in the dense reconstruction, that occurs between two rows that do not have a lot of overlap. Next to that screenshot is the dense reconstruction based on the "disabled" option. The errors are gone.
With 1.2.3. I can't get the two rows to align at all using the generic option. The "disabled" option on other hand aligns them without a problem and the dense reconstruction shows no errors.
The difference time wise is 7h 28min for disabled vs. 50min. for generic, which brings me back to my original question. Any chance on exposing the generic parameters (for example as advanced settings)?
Cheers!