There is an update that refers to this and more at this moment. The reason for the sudden push in 2.4 is due to some of the 2.4 features that were tested did wind up in 2.3.7, however, some key items and arrangements have been skipped.
One of the biggest request we've had next to deluge getting added was the means of separating their directories for ease of understanding what's what from those running both clients in tandem.
The update hre in the next 30 minutes will add the needed fix to your .rtorrent.rc file that will inform rtorrent to look inside of /torrents/rtorrent. This update however, will involve us to need to select all torrents and then right click, followed by 'Save to...' and then point them to save inside the rtorrent directory. We could do this automatically, however, it could cause issues and lead to dead/abandoned torrents and thus report the ratio (to you, not the tracker) as 0.
I will let you know when to run the update.
You should already be able to do the following to see some of these current changes, with a couple minor fixes following:
git checkout master && git pull
This should highlight some of the additional updates (you may see a lot).