Checking the rules for the petrified condition, Enlarge Person and for transmutation spells in general shows that there is nothing that mutually excludes both effects at once. Specifically, a petrified humanoid does not change type and become an "object" - it is still the creature, but with a condition applied.
There is no apparent "freezing" of ongoing effects, spell durations etc, which should really be noted under the condition if that was the case. There may even be undesirable exploits to make cheap permanent effects tied to petrified creatures under otherwise temporary effects.
So in my opinion, that supports your option 2:
(2) The petrification creates a statue of one's current form, but when
the spell wears off the new stone statue changes shape.
However, I think there is ample room for DM interpretation supporting either of the other two options, and even variations depending on what kind of effects can be "frozen in" when a character is petrified. It would be a minor ruling either way, and only require a little consistency during the game.
A side-effect of supporting option 2, is that if you cast any visible effect that does not affect normal objects on apparent statues, then you will see which ones are in fact petrified creatures from how the spell works (or not). As there is no competing "detect petrification" spell as far as I know, I think that is probably ok.