Canonically, the Jedi really did pass through the actual core of the planet. No, it wasn't just a cutesy Gungan folk-tale name for "some deep but physically plausible underwater caves that actually take you a few dozen miles or so". Naboo is geologically unique and an enigma to astrophysicists, in that it doesn't have a molten magma core. The planet is made of a porous conglomeration of large rocky bodies, permeated by caves and tunnels full of water.
Since we've established that the Trade Federation landed their invasion fleet on the opposite side of the planet to the capital city, going through the core really is the shortest route. It's a challenge that we have to go to such lengths to explain the logic behind something that is canonically part of the movie. But thankfully it all works in Sally-logic.
Obi-Wan: Hmmm. We're still stuck unless they give us some kind of transportation.
Qui-Gon: I told you we should have befriended the local fishermen.
Obi-Wan: Maybe we can barter your blasters for some hoverbikes?
GM: You're Jedi, you know. The class comes with Force Abilities. Check your character sheets.
Qui-Gon: Hey cool, my spell list has "Suggestion". I cast that!
GM: It's not a spell, it's a Force Ability.
Qui-Gon: I roll a 13. "You want to give us a transport."
Boss Nass: Yousa takes a bongo to helps yousa on your way.
Obi-Wan: What's a bongo?
Qui-Gon: It's a—
GM: Transport. You hope.
Obi-Wan: Now, how do we reach the Queen?
Jar Jar: Through da middles of da planet!
Boss Nass: Uh.. yes! That'sa right! The fastest way is through the planet core! Heh heh...
Obi-Wan: Looks like someone's cast Suggestion on the GM.