This project will not include a crosswalk at Naples Road. I hope it will not preclude it. However, the general thought is that the long-term solution there is going to be addressed as part of Comm Ave Phases 3&4. Packard's Corner currently only has crosswalks on 3 legs of the rather massive misshapen intersection. The next phase of Comm Ave will have a reworked Packard's Corner with (signalized) crosswalks on all 4 legs, to make it much more pedestrian friendly. While not quite as short a route to the supermarket as a Naples Road crosswalk, it may be the best we can get making the T happy about people crossing the tracks.
(Again, I'll note that here in Europe, there really isn't this crazy fear of people crossing tram tracks... it's just a tram. No need for fences or barriers. Comm Ave itself, with the speeding Masshole drivers, is much worse.)