When running pairToBed in output BedPE mode and type = either ( default)
a match on either read will output a BedPE entry line
a match on both reads will output 2 BedPE entries.

This seems logically inconsistent with the purpose of the tool, additionally it's not consistent with other match types.
For instance in type = neither. When 0 matches occur only 1 entry is output.

In Bam output mode this behaves as expected. Both read records are output consistently.

If you agree this is a logical bug, I'm happy to contribute a fix.

To be logically consistent it seems the result should never include multiple identical bedpe entry lines, because bedpe entry already encodes both pairs from the original paired input file.