Was the type of floor covering being planned known to the builder while
he was designing, planning and constructing the house?
Yes, the builder knew what areas were to be tiled.

If so, and the tile guy checked as I think you are now thinking he
should have, what would the tile guy have told you, and who would you
want to fix the substandard flooring? Obviously you think a few pounds
of additional nails or screws would solve the problem of the decking
being too thin to prevent it and possibly the joists from flexing?
He claimed he checked and all looked fine. However, being a little more
experienced now, I have noticed that they nailed the floor to the joists
with liquid nails. However, there were sections where the joist was missed.

Who
chose and specked the subfloor material and did the initial nailing?
My guess, the builder.

Why
nails if tile were to be used?
Dunno. Is that not code?

And without additional nails/screws,
wouldn't the original design "move" regardless of the type of floor
covering?
Yes, but it appears that only a hard surface like tile would be
affected...not carpet or even possibly vinyl flooring.