N9QTweak is simply a collection of scripts that doesn't interfere with anything else on its own...

Only when you apply a tweak will it affect the system so if you have any other app like Homescreen Settings/Billboard/LPS Magic installed its pretty obvious you shouldn't aim to do what those apps do via N9QTweak...

I'm using all of the above including Overclocking to 1150mhz except LPS magic [stopped using once Billboard came out] and fastern9 (uninstalled it as its too unreliable for me) and not a single reflash done...In fact except for updating fw several times [pr1.0 - pr1.1 - pr1.1.1 - pr1.2 - pr1.3] and 2 re-flashes in the beginning i don't remeber reflashing at all...AND i have been using many tweaks, themes (at one point had 19 of them), apps etc since i got my phone early November 2011...

Its all about knowing what you are doing instead of blindly doing them first...If you ever want to know what a package is doing to your system just uncompress the .deb file and read thru...Its pretty easy to read the N9QTweak master script too which gives you an idea of what it does instead of just plainly believing fiction...