Saturn,
As you can probably imagine, there is no single/simple answer. If you are working with a particular exhaust pipe (where the angles of the cones, and the distance between the front (divergent) and rear (convergent) cones are "fixed", that is one conversation. Another more involved way to look at the issue would be how the angles and relationships might need to change, depending on blowdown (in other word: a change in exhaust pipe could be in order).
If you look specifically at the distance of the rear cone to the piston/port face, increasing blowdown probably means lengthening the exhaust pipe -- and if you do the math, you will find that it may mean lengthening it significantly with a moderate increase in blowdown.
The reason for this is: Think of the distance to the rear cone being a function of the amount of time (or we can even say "degrees rotation") from exhaust *opening* to transfer *closing*. If blowdown is increased (by raising the exhaust and/or lowering the transfer ports), then the amount of degrees of crank rotation (exhaust opening to transfer closing) has increased. This is somewhat "independent" of how high the exhaust port is, since the sound wave that travels down/back in the pipe does not begin until the exhaust opens (regardless of how high or low it is).
Of course once again: if you are working with a particular exhaust pipe, lengthening the flex to put the convergent cone in the correct position may result in the front/divergent cone being too far away from the piston (exhaust port-face).
There is no clear simple answer -- but the short answer would be: if an engine is modified to increase blowdown, and you are working with a particular exhaust pipe, then the first thing to try would likely be lengthening the pipe. Do the math and you'll get a rough idea how much.
PM