Almost certain that all those behaviors are controlled by SOE's code. All EQ2MAP does is add POIs and maps (and via the in-game browser allow for submission of new POIs to EQ2MAP). The blinking behavior and the search behavior is all part of the map window is set to work by SOE.
As for clusters of POIs, way back in the day they used to get merged into one "cluster" type POI to address that but now there's few cases where they overlap so much that you can't tell any of them apart; it can be tricky to find exactly where to hover over to get the one you want, but I haven't seen any cases where it's not possible entirely (and even then, you usually just have to filter off some types: quest updates and "locations" are the worst offenders in terms of number).
__________________
|