We got in touch with the researcher for this route and this is his response to going off the bike trail/path:
The reason(s) that the current maps route riders to Clifton and later
re-join the bike path in S Charleston is to route people past the front door
of The National Afro American Museum and Cultural Center in Wilberforce.
The route also takes people closer to Massies Creek Cemetery where Martin
Delany is buried. Martin DeLany is known as the father of Black
Nationalism, he was active n the URR, was the first African American officer
in the US army, met with Lincoln in the White House and shared a strategy
for winning the war. The original marker for his grave was small and had
his name misspelled. The museum raised money for a more appropriate maker
for a person of his stature and they are very proud of the project. Another
reason for the current routing is that it takes people right through the
campuses of two HBCU's Wilberforce University and Central State University.
Both have supported riders using the route.
From a historical perspective I like the current routing. From a pure
cycling perspective of getting from point A to point B staying on the path
would make more sense. So those are the trade-offs.
I suspected it was a historical reason, but it's always nice to have confirmation.