Thrulines does not consider clusters of DNA matches. It just looks to see if any presumed ancestors of yours is a presumed ancestor in your matches' trees.
My grandmother was born out of wedlock, and Thrulines suggested the entire line of her biological mother's later husband (not her father) was her own. Simply because he was from the same area, and among my matches happened to be ones who shared parts of his ancestry - enough to suggest that all of his lines and he himself was my ancestor. But there was no intersection of those matches. The alleged common ancestors were pulled out of multiple matches' trees who weren't related to each other.
This is the big issue for newcomers, there is a process and quite a bit of knowledge to doing this properly. It is easy for newcomers to just pick something out of Thrulines or their matches, where there isn't really a connection.
In particular if most of your ancestry is in a very concentrated geographical area, this can seriously muddy the intersections/overlaps of the matches. I have so many matches that come up with shared matches from multiple clusters, from maternal and paternal sides. I even suspected that one of my lines had infidelity on it. But it's just that almost every DNA match from that line, was also a DNA match from another line. I also have a few closer matches who are matches on both lines, and it's been those that have been key for unsorting those intertwined lines.
