I've always felt that the Turbolift markers are there to provide an indication of direction rather than an accurate demonstration of decks passing by.
In a related note, there are relatively few occasions where we can actually use the time it takes from one location to another to accurately measure potential distances within the ship (since any Turbolift ride can be affected by other cars in the tubes). So, only on occassions where the ship is totally empty (Ultimate Computer
, By Any Other Name
) so we get any indication of how large the ship really is. But that's just for fun
With regards to the ship having "Deck 1" at the bottom, while it might help ease the issues in Day Of The Dove
and the whole "Deck 12" thing, it runs into problems when Kirk's quarters relocate to "Deck 5", as he's back in the Engineering Hull again! Also, Elaan of Troius
establish Sick Bay as being on "Deck 5" and "The safest place on the ship". If Deck 5 is in the centre of the saucer that statement makes sense - less so if "Deck 5" is in the Secondary Hull.
And so what if Deck 2 takes a long time to get to, even if below the bridge - maybe there was a traffic jam!