Thank you for your insightful question. I added a comment line in my original post, also copy / pasted below. You understand bioinfromatics plenty :) Your thoughts about how to go about this parsing , after my update? Thanks!

# A1 and B1 are not merged here because B1 and A2 overlap, and have no distance of separation between them, and therefore, the pairing of B1 with A2 is prioritized over pairing of B1 with A1