@The Arsonist:
- The permission issue has been resolved a few versions back.
- About the transmission application problems, I really cannot comment. I used it last time a year ago and it was in quite a bit of hog for my device. In general, even though I don't know the reasons and the exact details of this case, I would not exclude that some settings can amplify problems that transmission might have.

In my opinion, if you are using transmission you are not targeting anymore for low consumption and you can put the settings to default - there is a button in the version in testing for that. When your transfers are complete you can reapply the settings of your liking.

Finally, the application was done after a request of debernardis to assist the research of the optimum settings for those options. It is clear that the "proposed" cover only a part of the userbase and not all use cases. For example, if a user would like to push around large volumes of data regularly most probably the default settings are better or at least tested in more length for stability.
There is a place for users that don't really want to experiment of course, for those I would propose to use the interface to change just the swappiness value in something like 60 and only that.

Just to be clear, that is only my opinion and I'm not an expert in any way on kernel tweaking matters.