wow i cant belive nobody has said this yet.
okay im not sure how true this is but apperently there might be a HLE3. which( brace yourself for this one) would include the portal gun! in the begining (i asume) alyx explains to gordan that the lab that she got the gun from was somehow destroyed. well thats all i know. i think the portal gun was actually transported to them.
i suppose that would explain why Portal would be in the orange box.