For all other Starship operations, not having to coordinate with NASA and direct competitors (remember that conspiracy theory involving an ULA sniper? [1]) is a plus.
[1] https://www.washingtonpost.com/business/economy/implication-...
Lastly, given that Boca Chica was little more than a tiny retiree town, placing the facility there means they can buy up and develop all the land around it far more easily than picking some other coastal town.