-0, I agree nextMatePosition is rather implementation specific, in that it likely assumes you have an efficient way to go from reference positions to reads, as you do in reference sorted read file. One can imagine other ways of storing reads that don't use this reference ordering, but not sure if anyone cares about this.

If mapping to a reference graph structure rather than reference sequence, I think we can imagine how we'd translate the nextMatePosition field to a node within the graph. 

As a general comment, I agree with Adam, the more the reads data structures promote the reference in pure sequence terms, the harder any fork will be to move to a more general reference structure.