I believe Tstarnes will add them nearer to publication order, but will likely add a note to the issue saying when it occured chronologically if it's not merely a flashback issue. Untold Tales of Spider-Man is designed to fit between early spider-man issues, and I'm sure there are others of this sort.
Reason not everything is in that kind of order is that events change meaning and retcons would mean the origin is repeated many times, different every time and be completely irrelevant to the first few issues.
That is all correct. If you read the untold spider-man or x-men first class or lost x-men or any of those, they very often change the tone and intention of the original comics. I have tried to read chronological orders like that, and it is hard to read sometimes, since one of these "flashback" issues can invalidate what happened in the original comics where it was set. Something people sometimes get confused on, this isn't a straight chronological order, there are lots of those around the internet, this is meant to be a way to read through all of marvel in way that is enjoyable and makes sense.
There's also probably a way to create shortcuts to the comics, but be able to change the Order number assigned to it - Travis has to do this every time he moves comics around. I haven't the technical know-how, but I can't imagine it's hugely complex if you put your mind to it.
Actually, putting in comics way early in the order is easy. I have a system built so I can slide comics around and the renumbering on the site is all handled programatically.