Would the cylinder still work the same way if you pierce the edge at
400agl at 120 knots at 1 mile then 15-60 seconds later pull up to
500agl will the scoring program award you which ever is the more
advantageous score? [earlier vs higher?]

Like Hank said, you get the most advantageous score. Rules aside
though, I would hope any CD who saw this maneuver either in person or
on a trace would slap the pilot with a huge unsafe flying penalty.
Lots of gliders are finishing, and you can't see the guy behind and
above you who you just pulled up into -- and he can't see you either.
This isn't just theory. I have had a glider dive over the top of me
right at the finish cylinder, missing by 20 feet -- good thing I
didn't do any pulling up, or I wouldn't be here writing right now.
Please just cross the cylinder wall at your final glide speed, then
gently slow down and enter the pattern. The manever you describe also
wastes points -- the pilot would have done better by simply gliding at
90 knots to the cylinder wall.

John Cochrane.