we occasionally saw the pilot version with the taller bridge
Did we?
Totally. For example:
http://tos.trekcore.com/gallery/thumbnails.php?album=23
http://tos.trekcore.com/gallery/thumbnails.php?album=24&page=6
By the way, there's a catalog of all TOS Enterprise footage used on screen at http://www.trekplace.com/tosfxcatalog.html (thanks again, blssdwlf, for the link). The shot in question is called Cage Bridge (ironically enough) in this catalog.