Hi Andrew,
The main bypass can be anywhere in the system...doesn't matter too much. If it's real low on the car and set up very light, sometimes the weight of the fuel in the line above it can cause it to bleed down. It'll also lose a bunch more fuel when you change the pill if it's low. The 4-way shut-off idea is a good one! For just a few bucks more, you get an extra port that is always open on the shut-off for use as a main or high-speed port. If a person has to buy a new shut-off anyway, I always suggest a 4-way for that extra hole.
Generally, because the pump is rigidly fixed and the shut-off cable needs to pull on something solid, the shut-off is mounted directly into the pump outlet using a bulkhead fitting. Also, the Enderle-type shut-offs don't have a means of attachment to the chassis or anything like that. Flopping around mid-stream in a hose might not work well. If you can come up with a creative way to mount that shut-off, it should work well where ever you put it.
I think if it's down low on the motor with the pump, it may shorten a bunch of your return lines vs. being mounted up higher on the motor.
Have fun plumbing!
Spud