Every municipality is different when it comes to overnight/long term parking. Although I don't know the circumstances at Harvard, most stations along RI do not have designated spots for overnight parking... however stations at Orland/Laraway Rd./Manhattan do. The one thing these stations have in common are the electronic parking machines, while the old fold-up dollar boxes still remain along RI. You may even be better off contacting Harvard police, if they are the ones who patrol the lot... they may be more help than the ticket agent.
From Metra's Site:
Station Parking Contact
815-943-6468
815-943-4431 (Harvard Police)