Well, if you listened to it twice 50%, give it one count up lol
It's easy, set loop mode on single track and click in the very end of the time slider repeatedly till your count is correct from your playing session
To me, I skip tracks in that way, too, but really, to me those few lost counts are not THAT important.
Sure, play counts don't work 100% correctly in that way, but still very fine and are still excellent in finding your personal charts, determining automatic synchs, etc...
Also they aid the statistic Nazi in me as I said before
Now, with other media for example, this is less of a problem: movies and tv shows you normally watch in full and if not, their playback position is saved for your convenience to pick up later or at least see that you only partially played it.
I like your OCD way of doing things, reminds me a lot of me lol