Are you sure you don't have that backwards? As presented, it doesn't makes sense. RER will display (typical modern EMU v Diesel Loco hauled carriage) twice the rate of acceleration and braking, and subsequently a geometric advantage in terms of performance for stop/go over loco hauled.
I'd say Lawrence and additional stops are far more readily absorbed in timetables when run EMU.
Not only that, but when you run an RER type service you then bypass all trains from the outer network through these areas.
The platforms for the new stations like Lawrence East station won't even fit a regular GO train! They couldn't stop there if they wanted.
So the report saying that these stations would negatively affect the timetables of trains coming from the outer network is absurd.
If anything, it will allow the trains to bypass all downtown stations serviced by RER and INCREASE their speed and time it takes to get downtown.
However stations exist within the RER system will have no affect on these trains.
They will have an affect on the RER system, but the RER system is intended to be a "subway-like' regional rail system, not a commuter train.
Its intention is to make many stops. The furthest it will come from (Unionville in the case of the Stouffville line, and Aurora in the case of the Barrie Line) will be a short hop, and will be increased in speed from current travel times, like you said Steve, by the EMU equipment.
Something is fishy.