Yes, the pre-CBS Fender J bridge pu being closer to the neck pu had its upper 2 flanges (where it's screwed in) exposed above the bridge cover. I'm sure Leo & co were only thinking about covering the bridge, the original mute and sorta the pu with that huge cover/"ashtray" and weren't especially anal-retentive about it. (OCD hadn't been invented yet...) But the suits at CBS (according to "folk lore") who knew nothing wanted the visuals "cleaned-up" and so the pu was shifted south to completely hide under the cover.
Now.., if you just move the bridge south which they first did, the saddles which were originally more centrally staggered will then end up at the top of the bridge plate requiring a longer bolt for the G-string saddle. (which was overkill IMO) There aren't thoroughly documented hard-facts from that time, but let's just say things went down in the factory during the early transition from Fender to CBS/Fender.