I generally leave the mufflers ON and always on the street for the Charger, and mufflers always on the Jeep CJ5.

The Moroso Instructions are fairly explicit about placement of the pipe.

DRAG RACE APPLICATION
1. Remove valve covers and drill a 1-1/8” hole in each cover. On all Moroso “Stamped” Valve Covers, the holes provided will work perfectly. When determining hole location for all other covers, try to find a flat surface that is not directly over a rocker arm oil hole.
NOTE: Separators must be installed in a position at right angles to the top of the valve covers to function effectively. See Fig (1)
2. Before installing rubber grommets, remember to cut the bottom ”seal area” off to allow the separator to work. Lubricate the inner surface of the grommet with a touch of oil or grease and twist in the separator. The fit should be tight to help hold crankcase vacuum.
3. Drill a 7/8” hole in the right and left collector directly behind the transition area shown in figure (2). Check valve installs on the top of the collector.
4. Place check valve probe at the proper depth and angle per drawing and weld all the way around for a complete seal.
5. Use a 5/8” high heat or high pressure hose to complete installation. See Fig (3)

I suppose you could experiment with trying to mount the Pipe as near the flange as possible and with a short collector it might work, but then again, it may not be very effective as compared to having the Pipe at the merge-point where all the header tubes meet in the collector.

I know it was a fair amount of work to remove and drill holes in almost New headers, but though I had similar thoughts about mounting the pan Evac pipe in the exhaust pipe instead, from all I read, I didn't think that would be sufficiently effective. Since this isn't a true vacuum pump, I figured I needed the best pipe placement possible and mounting it in the collector was the only recommended placement. I didn't want to go to all that trouble and have it not work.