Presupposes that deck 2 is directly under the bridge. Was there ever a TOS canon reference to the bridge as deck 1?
Not on air. But
The Making of Star Trek (1968) describes the decks in a way that Franz Joseph followed very closely, including putting 1 at the top, if I recall.
This line of thought was more or less confirmed in TMP and the movies, with the bridge as "A-Deck". However, this is TOS so I thought it might be fun to look at dialogue in the show related to this issue.
MUDD'S WOMEN
(Spock and MW walk from the Transporter Room to a turbolift)
SPOCK: Deck twelve.
(they go up several decks)
ENEMY WITHIN
(GT Fisher has just run out of Rand's cabin)
FISHER: Deck twelve, section--
DAGGER OF THE MIND
(Van Gelder has been spotted wearing an Engineering jumpsuit in the wrong area of the ship)
UHURA: Captain, section C deck fourteen, reporting trouble. Someone in Engineering uniform.
KIRK: Security control, this is the Bridge. Come in.
SPOCK: I have them, Captain. Closing off deck fourteen, search in progress.
I wanted to get these out of the way because they seem to belong to the notion of the 20-deck thick saucer Enterprise (Deck 12 would be the widest part). Of special note is the fact that an Engineer would dare to be wandering around the saucer! Back to your pit, slave!!!
These dialogue references cause trouble for many, since Deck 12 would be somewhere in the Pylon if the decks were counted down from the Bridge (my solution is simply to ignore the pylon, its mostly girders and support struts anyway). And speaking of oddities in terminology:
CONSCIENCE OF THE KING
SECURITY: Captain? Security, H deck, The weapons locker has been broken into. One phaser is missing.
COURT MARTIAL
STONE: Finney.
KIRK; Localise that.
SPOCK: B deck, in or near Engineering.
KIRK: Seal off B deck, sections 18Y through 23D
While its possible that letters are being used to represent decks,
Robert_Comsol offered a more plausible solution in the form of (B)erthing Deck and (H)angar Deck. Certainly, the alphabetical system is not heard from again until the movies.
ERRAND OF MERCY
(The Enterprise is struck by several energy blasts in the lower saucer area)
SPOCK: Blast damage in decks ten and eleven, minor buckling in the antimatter pods, casualties very light.
CITY ON THE EDGE OF FOREVER
(Mad McCoy has just left the Bridge)
KIRK: Continue alert, decks four through eleven.
Both these quotes strongly indicate an 11-deck saucer, with the first 3 decks at the top (and being smaller are more easily confirmed to be free of Mad McCoy) and some sort of anti-matter containment at the bottom (near the weapons systems, so makes sense)
AMOK TIME
(Kirk and Spock exit the Bridge, heading for Sickbay)
KIRK: Deck five. You've changed course for Vulcan, Mister Spock. Why?
MIRROR MIRROR
(Kirk and Chekov exit the Bridge)
KIRK: I shall be in my quarters.
...
CHEKOV: Deck five, sir?
(Kirk nods)
ULTIMATE COMPUTER
SCOTT: Captain, power shutdowns on deck four. Lights, environmental control.
...
SCOTT: The power's gone off on deck five.
...
DAYSTROM: Decks four and six are living quarters, are they not?
KIRK: Yes, that's correct.
ELAAN OF TROYIUS
(Kirk and Elaan exit the Bridge)
KIRK: I want you to go to Sickbay. It's the best protected part of the ship.
...
KIRK: Deck five.
LET THAT BE YOUR LAST BATTLEFIELD
BELE: You're the captain.
KIRK: Yes, I am. I think we can consider your problem settled. At least for the present. I have ordered guest quarters for you on deck six.
If Decks 5 and 6 are the widest part of the saucer then the centre (where Sickbay is) should indeed be the safest part of the ship. It also makes sense to spread the most living quarters around in this area. If Decks 5 and 6 were counted from the bottom of the secondary hull then there would considerably less space and that is before things like shuttle facilities and deflector machinery (which we know are there from the external view) are taken into account. Again, strong indications that deck numbering starts from the top of the saucer.
The following dialogue is from the first episode, where a half mile Enterprise may still have been in mind:
CORBOMITE MANEUVER
(Bailey is running a battle drill)
BAILEY: On the double, deck five! Give me a green light.
...
BAILEY [OC]: Engineering, deck five, report. Phaser crews, come on, let's get with it.
However, we then get this snippet from the Animated Series!
TIME TRAP
SPOCK: Where are you supposed to be working?
KLINGON: Engineering, deck five.
SPOCK: Captain, allow me to escort this young man to his work area.
A lot of early dialogue referred to "decks and Engineering Levels", indicating that the secondary hull had "levels" while the term "deck" was reserved for the saucer. However, as time went on the terms became more interchangeable, especially as several episodes point to the presence of one or more Engine Rooms in the saucer as well:
DAY OF THE DOVE
(Bulkheads to the "lower decks" have closed, trapping 392 people)
SPOCK: The Klingons control deck six and starboard deck seven, while we control all sections above.
(The Engine Room is still accessible however)
And finally:
ENTERPRISE INCIDENT
(Spock and Romulan exit the Bridge)
SPOCK: Deck two.
As mentioned upthread we don't actually see the motion lights, so Spock could well have pressed the "hold" button while he finished his conversation. There are a couple of other theories on the BBS as well that make good sense, but suffice to say that Spock's "Deck 2" isn't a deal breaker.
So in summary; nothing concrete, but a lot of strong indications that decks are numbered from the top of the saucer down. It could work the other round but requires a lot more mental gymnastics.
I'm not sure I agree with the mental gymnastics to do the flip since you are inventing/retconning a hold button for TEI. The lettered decks could be taken as engineering hull deck nomenclature. Otherwise, at eleven decks thick, all the verbal deck references are in the primary hull (save deck 12.)
You might even be able to fit four Warped9-sized shuttlecraft in it.
(oh, FYI, if the yellow is deck 1, then the red bar is deck 11. 
)
