Adding the alternative readers has no effect on the original readers. In fact the most common way to start the alternate readers is by selecting a launching PNG image file, in the same manner that you select books within the original software.
KOreader started as a project to provide an improved PDF reader for Kindles, the PDF rendering is done using "MuPDF" code. Try it out, I don't read that much PDF on my AuraHD so I can't talk about it's performance but some have said that it is much better than the one from Kobo.
Luck;
Ken
KOreader does reflow, and it's features are always improving, so if there is something you found lacking check back at
https://github.com/koreader/koreader and see if it is listed for merger into the next build.
No reboot required for all the recent builds.
While they try to have it working in all the eink Kobo eReaders, some of the earlier models, like the early Touch models, seem to have more issues than the newer devices like the AuraHD.
An install guide.