A couple months ago, I called MBTA police to report a courier(?) bag stuffed behind a news box in Central Square.

A transparent newsbox would have made the bag more visible from the sidewalk in that particular situation. I imagine there's still only a small random likelihood that someone would have noticed and reported it in a timely manner.

Keeping these transparent boxes clean of trash, graffiti, postering, and damage will help passersby notice suspicious objects inside, beneath, or behind the boxes.

it's not just about "homeland security", folks (although we know from past incidents around the world that opaque newspaper boxes and trash barrels are favored depositories for bombs).
There are all kinds of other things that can be secreted (yes that is a verb, and it doesn't have anything to do with fluids) in opaque boxes placed in high traffic areas. for example, such boxes have been used to facilitate drug deals and the transfer of other contraband. Now while I am certainly not going to suggest that a terrorist attack could not happen at a T stop (I think that people in Tokyo and London could, unfortunately, speak to that), i actually think the policy is more effective against more mundane crime, e.g., drug dealing. this, of course, is a good thing, because where there are drug deals, there is the always the possibility of one going bad and innocent people like you and me being in the middle of it when it does.
Clear boxes are a non-intrusive and low cost anti-crime measure.

People dump all sorts of inappropriate things in public places and public trash cans - TVs and CRTs, jugs of used oil, waste chemicals, tires. Some of these things can be very dangerously toxic or explosive (which is why they are expensive to dispose of properly). Clear boxes and barrels can prevent an otherwise easy hide.

Funny. The Metro was forced to change to clear-bottom boxes a while back - why so long for other publications? Why do the Globe and Herald seem to be immune from these requirements? hmmmm