Can you leave it in the top hole? Yes. Is that the correct location? No!
I am at a loss why aftermarket companies are not making the correct brackets so the push rod will fit into the lower hole, as it should.
Pedal ratio is very specific regarding manual or power brakes and if you use the top hole on a power setup, you are leaving a LOT of your braking power on the table AND you are having to push your pedal further than you should be.
I am dealing with this on the wagon I just bought. In the top hole my brake "work" but I cannot get the wheels to lock up and have to push it way further than I should, to the point my shoe hits the gas pedal accidentally at times. I moved the rod to the lower hole and it was amazing how much more power I have, less travel of the pedal and a better feel to it. Downside is the rod is at a bad angle.
My plan is to do what I have seen done on other systems, where a bracket (thick flat plate with 2 holes in it) to basically build an "offset" rod. Bolt the plate to the push rod of the booster in the upper hole and the clevis into the lower hole, making a "Z" bar. This allows the correct hole in the pedal to be used but keeps the push rod in the right alignment. When I am back from vacation, I will do it and post up pics for others.