No direct indication on the size of the planet, except that it had Earth gravity. Clearly, the Ba'ku hadn't seen any benefit in spreading themselves out, and only inhabited something like one billionth of the dry surface area.
As for why the Feds didn't realize right away that these couldn't be natives... We could argue that they did. The only hints that Starfleet would have thought of the Ba'ku as "primitive aborigines" come from the library scene that was deleted from the final movie. In the released version of the film, the Feds could easily have been aware of the interstellar origins of the Ba'ku, but would still have seen the need for covert rather than overt study - it would have been the prerogative of the Ba'ku to give up their interstellar lifestyle and to revert to "primitive" farmers, apparently several generations ago, and disruption of this lifestyle would and should not be the Starfleet way. After all, Starfleet didn't want to disturb the similarly pastoral and isolated folks in "Paradise Syndrome", either, despite them clearly being non-native to their planet.
Picard personally didn't know at first that the locals were tech-savvy, but he might simply have been lax in reading the material, or not privy to all of the material. And since apparently only a small cabal in Starfleet knew that the Ba'ku were extremely long-lived, Picard and others would have to assume that the people currently living on the planet would be so many generations removed from the original interstellar colonists that they would have forgotten how to build a lightbulb, let alone a warp drive. Especially if the Son'a presented them with their own "findings" on the matter, and the Ba'ku didn't actively promote a different view through their everyday activities.
Nobody ever really raised the point of whether the Ba'ku were "natives" to the planet, or "immigrants" or perhaps "vagrants". Picard argued from the emotional point of view that the planet was their home, without regard to whether it was "ancestral" or newly acquired. Dougherty dismissed the entire point, again without regard to the age or nature of the claim.
Timo Saloniemi