The whole point of filing retirement paperwork is to start reaping the benefits, like the MLB pension, that come with it, right?
I don't know if the rules allow for a player to announce his retirement and then be released by the team so he can collect the remaining money owed to him. That seems a little fishy to me and would probably not be the greatest of looks, not to mention I could see the MLBPA having a problem with that sequence of events. Plus, the team has a interest in not paying him the remaining $25M if he's not going to ever be a productive player again. He was not a Dombrowski guy and Dombrowski runs the baseball ops, so he has no long-term relationship with Pedroia, meaning he has no real motivation beyond some kind of warped sense of "doing the right thing" for a player that hasn't been a meaningful contributor to the team in a couple of years, basically since he's been here. And that may be cold, but it's also reality and he has the dubious position of having to make that call.
The Red Sox lose nothing by allowing him to continue to try to rehab for as long as he wants, but if there's no light at the end of the tunnel after this season they're going to have to tell him it's time to sign the paperwork or they're going to have to let him go. The latter scenario means paying him the money so I think they want him to figure it out on his own. Two lost seasons (more if you count the time he lost when the injury first occurred) might be enough to convince him that it's time to do the honorable thing and not hold the organization up for money he's never going to truly earn.
Pedroia is stubborn enough to never want to admit defeat, though, so this has the potential to get ugly in a few months. Here's hoping it doesn't.