RTD's scripts are fairly notorious for the lack of rules and structure. All of his scripts contain an abundance of contradictions, so it's impossible to really tell what he was trying to say about the Time War. It's possible he did intend on the Ninth Doctor being the Time War Doctor, but simply forgot he included the mirror scene in Rose.
I mean, apparently the time lock was impossible to breach. But then like.. it wasn't and anything could get through as long as it was small?
The guy loved to write people on council estates referencing celebrities and discussing knickers, but have him write a sci-fi storyline and you're kinda fucked.