From the way the configurator is structured, it looks like the Performance option really is an option, and you add it to the base car. WA has a $42.5k limit for its incentive, but even though all Model 3's being shipped now are at least $49k, they all qualify, because we just added options to the base price.
However, most states with a qualified incentive also have official lists of which cars qualify, and that will take precedence over anything Tesla does or says. The Massachusetts list is HERE. It looks like they do include the 3, and don't specify a version, price or options. Heck, they include the S and X too, but at a far lower amount.
A bigger concern might be that funding is limited, and it's first-come-first-serve, so you have to make sure that there is funding available when the car is delivered. You also have to keep the car in Massachusetts for at least 3 years.