The current configuration allows for an accessible transfer between platforms - there's a single fare control area for both directions.
I suspect the behind-the-scenes reasoning goes like this:
1912-built viaduct needs reconstruction since it's 111 years old; station platforms need repair since the were built poorly
The station work is substantial enough to trigger code compliance needs - most notably, having a second egress point
There's no way you can have an emergency exit directly onto the traffic lanes, so there's only one place you can put it
Might as well make it a public entrance - it'll make the construction/cost, and possibly the alterations to the historic structure, more palatable.
It's certainly not a bad thing to have the second entrance. It's far from the the most valuable to add, but it will improve access to the Esplanade (getting from the station to Francis Appleton Bridge will be 1 crosswalk instead of 4) and to the west side of Charles Street.
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A secondary entrance would be invaluable for the eventual construction of a red-blue connector whatever form it takes. Perhaps it would also allow the T to minimize construction time by letting construction workers occupy more space for their work.
I also know some Cambridge waterfront workers who come from Downtown and South Station CR who yeet at Charles in the mornings to enjoy the walk over to their offices because it's about as far from Kendall - especially north of the bridge. In the afternoons, they seem to not have a preference for Charles or Kendall - rather, chose which station based on weather, fatigue, etc. Would definitely help them out and maybe get a few more folks to exit a stop earlier.