They are correct about the unequal toll rates. The rates in the Philly area are much higher on a per-mile basis. Not sure if this is deliberate (like the NJ Turnpike near NYC) or if it was just based on the revenue projections at the time each section was opened, like they said.
The E-ZPass toll from New Stanton to Breezewood is $12.10, which comes out to about 14 cents/mile. However, the toll from Valley Forge to Bensalem is $5.40, or about 21.6 cents/mile. If the rates were equal (say using the 14 cent/mile rate), the Valley Forge-Bensalem toll would be about $3.60, or $1.80 less. Of course, everything depends on the per-mile rate the PTC settles on.