Actually, sometimes wiping /system does matter. Most of ROMs nowadays are smartly designed so GApps can survive OTA update. Because of that, sometimes when you flash a new ROM, script thinks that you are attempting ota update instead of clean install, so some things remain untouched. I'm not just talking here, I experienced that. I changed DPI in one ROM (SlimKat), clean installed totally new one (PA 4.4.4), and DPI remained like I set it on SlimKat. I reflashed again, this time wiping /system also, and it fixed things.
Morale of this story is that, while not obligatory (because ROM zips are supposed to wipe /system themselves prior flashing), it wouldn't hurt to do it yourself. After all, it's just another tick in TWRP