I changed the OP to say don't flash in bootstrap cause its not working. to answer your question though it seems to be "flashing" fine but its not actually deleting the system partition...so when it goes to put all the files from the rom in there there isnt enough room. BUT, and thats a big but, if you FORMAT the system partition then flash the rom it still "flashes" fine but then doesnt add anything to the system partition from the rom...this in turn soft bricks you and you have to HoB back to stock. Therefore i say again PLEASE DON'T FLASH IN BOOTSTRAP FOR THE TIME BEING! Luckily you seemed to have only did wipe data/factory reset and/or wiped cache/dalvik which means you really didn't do anything to your phone seeing as it didnt flash. Thus, you see all the same stuff in there cause it IS the same. Hope this answers your question, but if you want to flash in safestrap on safe side please go for it! Works fine that way for some reason...Thanks for posting the issue though! I like to know what i can fix for you guys to have a kick arse rom! (bootstrap fix to come!)
Yeah, that is what happened to me. I did notice that after i formatted /system the first time the flash was extremely quick, especially on the system partition part. So what you said seems to be true. Seems very odd to me. Good luck getting it fixed I would love to flash in bootstrap I'll even test it out for you