This is a great discussion...
After watching the movie I was a little annoyed that Scorponok never transformed into anything! (Sure, the toy version has a robot mode, and thats fine, but I think many of us would agree that his robot mode is a toy-based idea, and not how he was intended to transform in the movie...
If you didn't already, read that stuff on Ben Proctor's site... He talks about designing the scorpion, but doesn't even mention taking into account a transformation...
http://www.benprocter.com/SITEv2/HTML/PROJPAGE_Trans_08.html#Then look at his photos linked here...
http://www.benprocter.com/SITEv2/Graphics_Content/ZOOMPIC_Trans_Scorponok_ColorTexRefCombo.jpgScorponok clearly has the the "002" marking above his leg, that was on the side of the helicopter.
This would imply:
A) Somehow Scorponok "magically" does transform into a portion of Blackout. Prowl_83's idea has merit.
B) Or when protoform Blackout first scanned a Pave-low some of the detailing he absorbed effected his "pet"
Before looking at those photos, I would have gone along with the idea that Scorponok transformed into some kind of canister inside of Blackout, but those markings are from an aircraft, not a box of any kind.
The real answer is... there is no answer. His transformation was not shown in the movie because they NEVER DESIGNED one that works! Much like Frenzy, who "magically" transforms into a boombox, (yet has no boombox detailing when he's a robot.)