Long Running Merge sadly hearkens back to the day when mobile sales folks were the primary consumers of merge-replication. Consequently, this warning/alert is almost USELESS when dealing with more-or-less continually connected servers.
Stated differently, this warning is configured via Replication Monitor in the 'Warnings' tab - where you specify a time threshold in minutes.
So, say I set up a threshold of 10 minutes - for LAN connectivity. What that means is that I want to be WARNED when a Merge Replication agent has been connected for LONGER than 10 minutes. In the case of a laptop connected over a VPN from a hotel, it might make sense to see that they're taking > 10 minutes to synchronize. Sadly, if we're talking about a dedicated merge agent that's been running for hours or days, then this will ALWAYs be on.
All this said, I'm BASING the above statements on 2 things:
a) an INSANE dearth of documentation on exactly what this stuff means. I've googled and looking in gobs of books and only ever found this:
http://www.kendalvandyke.com/2008/10/difference-between-long-merge-and-slow.html
b) a simple set of tests where I created a new/simple publication and then once it was up and running, I set the threshold to 5 minutes. Sure enough, after the publication had been successfully synchronizing for 5+ minutes, the status switch to 'long running merge'
So, while I'm not 100% positive of my answer, I'm fairly confident it's correct.
Likewise, in playing around with the rows merged/second threshold it looks like those too are geared primarily at 'older' disconnected/reconnected merge scenarios rather than 'always connected' situations that are much more common today (thereby making them relatively useless as a monitoring mechanism as well).