Johnny B. Goode take 3 isn't - I mean take 3

Because it probably is his most important recording, Johnny B. Goode has been the topic of several comments and discussions in this blog before. (see here and here)
Common knowledge is that besides the well-known version as released in 1958, there is a so-called alternate version "Take 2/3" which consists of a short version of the famous guitar intro (take 2) followed by some studio talk and then continuing into a complete track (take 3).
On the HIP-O-Select 4-CD set of same name (HIP-O-Select B0009473-02) one can listen to both versions one after the other (CD 2, tracks 20 and 21). And if you listen carefully you will notice that take 3 and the finally released version are exactly the same recording. As Fred Rothwell explained in this blog, common practice for Berry was to play the intro and the rhythm first, while further lead guitar segments were overdubbed later. Thus track 20 (take 3) on the HIP-O-Select CD is the undubbed version and track 21 is the overdubbed version.
That's what common knowledge said. But then I received an email from a reader of this site who noticed something strange. Josep Rulló from Barcelona/Spain wrote:

We are missing the complete alternate take first used in the “Rock´n´Roll Rarities” album in the 1986. This complete take, identified as take 3, is very noticeably different from the master.
I mean, it´s great to have the basic track for the master (the undubbed master take), but I think somebody really got their wires crossed at Hip-O regarding this. Why did they leave the excellent alternate take out and, what´s more, splice the undubbed master take after the “Johnny B. Goode, take 3” voice?. They could have included everything as a great sequence that would have shown the recording process very clearly.

What Josep did - and none of the other collectors including me - was to compare the "Take 2/3" track on the HIP-O-Select box with the "Take 2/3" track as originally released by MCA/CHESS in 1986 on the double album "Rock'n'Roll Rarities" (Chess LP 92521). And when you compare these two, you will notice some minor differences and some major differences.
The minor differences are an additional false start of take 2 on the 1986 version, which is missing on the 2008 version which in turn has Leonard Chess shouting "Johnny B. Goode, take 2" at the beginning.
The major difference is that the 1986 version of take 3 is a COMPLETELY DIFFERENT RECORDING from the take 3 on the 2008 CD. It has a much longer and different piano solo between the second and third verse which you can easily use to tell the versions apart.
I wonder if someone can shed some more light on this. So far this is my theory:
When Steve Hoffman of MCA/CHESS created the "Rock'n'Roll Rarities" album, he not only remixed some of the 1960s recordings. He and his team also found an unreleased version of Johnny B. Goode and some studio chatter about the recording of the song. So they took the aborted take 2, the following discussion, and the unreleased version (rumor goes that this is take 1) and combined those to what they called a "previously unreleased version". Note that they did not claim the unreleased take to be take 3. They just moved it after the studio discussion, not before. And because that studio talk ended with Len Chess introducing "Take 3" we all came to believe that the unreleased take was indeed take 3.
As it seems, this also fooled the engineers at Universal when they compiled the so-called "complete" CD set. They were supposed to add takes 2 and 3, so they took the master tapes and used takes 2 and 3 - the real takes 2 and 3. This is how the real take 3, which by incident is the undubbed master of the hit version, went into production. They clipped off the false start from take 2 (bad) and added Len Chess's introduction (good). But no-one noticed that the complete track was notably different from the 1986 version.
Thus we have to note that there are these studio versions of Johnny B. Goode:

• Take 1: Recorded on January 6th, 1958. This was first released in 1986 on "Rock'n'Roll Rarities" as the second part of the so-called unreleased version
• Take 2 incl. false start: Again first released on "Rock'n'Roll Rarities", this is the first part of the so-called unreleased version
• Take 2 incl. announcement: First released in 2008 on the HIP-O-Select boxset, again this is the first part of the so-called "Take 2/3" but has the false start replaced with a spoken introduction
• Take 3 without lead guitar: First released on the Hip-O-Select boxset as the second part of the "Take 2/3" track
• Take 3 with overdubbed lead guitar: First released in 1958 on CHESS single 1691 this is the well-known hit version
• Mercury version: Just for completeness - There exists another studio recording made on September 21st, 1966 and first released in 1967 on "Golden Hits" (Mercury MG-21103). This can be easily identified by the use of tambourine and saxophone.

We have to say a big THANK YOU to Josep twice: First for finding out the differences, and second for telling us!