Having lived and used transit in both cities, I think the report glossed over some issues with SEPTA and made it seem better than it really is. Of course it is true SEPTA has not had some of the glaring problems that MBTA has had recently such as Orange Line trains catching fire, etc.
However I think the systems are different in a number of ways which makes it a bit more of an apples to oranges comparison.
For one thing Philadelphia is a much bigger city than Boston yet the rapid transit portion of the system (Broad St Subway, Market Frankford El, subway surface trolley tunnel, and PATCO line) is if anything smaller than Boston's equivalent. One might even question whether the subway surface trolleys can be called rapid transit since the surface portions are conventional streetcars running in the street with traffic whereas the majority of Boston's Green Line is separated from traffic (except the extreme end of the E line). Another factor somewhat glossed over in the report was the perception of crime on the SEPTA transit system. I know when I lived there a lot of people would not even go on the Broad St. line even in the daytime. I never saw this kind of attitude in Boston.
On the other hand SEPTA has an extensive electrified Regional Rail system much more extensive and with better service frequency than Boston's commuter rail, which seems more oriented towards bringing commuters into the city. SEPTA also has the tunnel so that trips can be made suburb to suburb from the western to the Northern suburbs which is more difficult in Boston due to the lack of the North South Rail Link.
I would summarize by saying for a suburban commuter SEPTA is superior but for someone living in the city Boston probably has the better system even with its well publicized problems.
That is a fair assessment as the Center City Tunnel which while being constructed was considered a boondoggle 40 years ago transformed downtown, especially Lower Market St.
The BSL is what it is..... and nobody has an answer for the Broad–Ridge Spur.