As Jan says, USFM treats section headings as being part of the previous verse. Paratext, for better or worse, follows the standard here. So I'm not sure there's a good workaround.
I'll say here that while I understand the logic of USFM from a technical/logical/computer programming aspect, from an actual user aspect I think it's wrong and unhelpful. I think almost anyone's natural inclination is to link the section heading with the following verse, not the previous one. This is one of those flaws I wish could be fixed in the underlying spec.
I do kind of question whether when you go to do final print, if you'll really want the print ranges and/or quotations present when the footnote is in a section heading. In other words, do you really want both the \fr and the \fq markers added to those footnotes? (Both are technically optional.)