Modifying the root filesystem is always a risk. In newer firmware, the browser might be used for displaying things besides the "browser app". So handle everything with care.
What I had in mind was to make backups of the files you are modifying, like e.g. the mesquite binary. Probably you won't need strictly all things from root. But then it might provide an interesting overview over the system.
PS: Yep, I'm a dev of Koreader - and you're welcome, of course. I have to add that others were much more active lately when it comes to contributing. It's become a community effort (thankfully!).