I've been obsessed with the details of this bass for well over a year and I have to respectfully disagree - I think the earlier EB0 and the later EB3 were not the same bass.
In those early years Phil went through basses like Bobby went through guitars in the 70's and 80's, and he rarely keeps his basses once he's bored with them.
In order to make a 60's EB0 match the details of the bass in the pics above they would have had to:
1. Swap the 3-ply pickguard for a 5 ply one.
2. Rout for the 2nd pickup in exactly the right location - the Hagstrom/DarkStar is wider but after much debate and study with my dad, determining the scale of the pics using the distances between the frets as a known distance and comparing it to measurements from currently-produced EB3s, the distance between the Hagstrom and bridge matches the distance between the Gibson mini-humbucker and bridge. The far edge of the pickup rout on a current Gibson and on Phil's EB-whatever are both 28 1/4 from the nut.
3. Drill three holes for the two additional knobs and the Varitone switch in exactly the right places for 1969-70 EB3 specs.
4. Possibly replace the bridge - I don't have SFTS in front of me but the main tray of the bridge on Phil's is exactly right for a 1969 bass. Gibson changed their bass bridge designs extremely often in the 60's - probably because they were all bad designs!
I especially can't imagine them bothering to do 1 and 3. I think they'd have left the 3 ply pickguard on it and drilled the extra knob holes wherever they felt like it.
This website has awesome details about historical Gibson basses:
http://www.flyguitars.com/gibson/bass/ it's been my main resource for getting the historically accurate restoration-type details right.