The possible answer from the tech support team is that merge or without merge must give same response, but
meshing in older version of ADS might end up giving slightly different response. It is recommended to always Flatten & Merge the layout components as that would be much closer to how actual PCB will behave in real world.
Hmmm ... I don't agree with that answer from support. If the extra edge causes a finer mesh at that junction between the lines, and if that mesh density change causes a change in results, then the finer mesh result should be considered more accurate.