The scored option (you might guess from its name) creates a synchronisation point when a certain score (100) is reached. Mostly this is so that you can decide that column A is more important that L or R in a polyglot.
A little-publicised fact is that the scores it gives are (a) exposed in {project}/shared/{config}/merge-normal.cfg and (b) that file, once generated is EDITABLE.
Unfortunately it hadn't not occurred to me before today that some people might want to match other paragraphs, but not line up q1/q2 etc, so you can't turn off specific markers yet. If, however, you are willing to sacrifice mid-verse paragraphs, you can find the line that says:
MIDVERSEPAR and set it to 0. From that point in time on (until you turn it back on or delete the file) it will not try to synchronise text at mid-verse paragraphs, which includes many "\q2"s, I expect