Are docked ships considered to be on the board (inside the ship they are docked to) for the purposes of abilities like Boba Fett's?

Example would be, Boba shooting at a Gozanti with 2 Tie Fighters docked, at range 1. Does Boba get to reroll 3 dice or just 1 die?

Nope. Docked ships and their equipped upgrades have no effect on the game unless there is another card in play that says otherwise (Ghost title is the only current card that does).