While attempting to create an unfiltered .pto for testing, specifying the --loopanalyze option still seemed to perform filtering. For example:
./cvfind --detect orb --pattern lrtb --rowsize 20 --overlap 30 --hugin --cellsize 50 --loopanalysis -o out.pto in.pto
Resulted in may pairs being dropped, apparently because of loop homography failing to find valid loops.