The AC does not negate the requirement to avoid obstacles with an engine inoperative and to read it that way falls short. The AC simply describes the basics for the design of departures for third parties. It does however describe the underlying requirements.
From AC 120-91
10. METHODS OF ANALYSIS. Sections 121.189, 135.379, and 135.398 require that the net takeoff flightpath clears all obstacles by either 35 feet vertically or 200 feet laterally inside the airport boundary, or 300 feet laterally outside the airport boundary.
The one engine inoperative requirement is harder to find but is present in the CFRs quoted in the AC. The first one for example, 121.189 states (among other things):
2) In the case of an airplane certificated after September 30, 1958 (SR 422A, 422B), that allows a net takeoff flight path that clears all obstacles either by a height of at least 35 feet vertically, or by at least 200 feet horizontally within the airport boundaries and by at least 300 feet horizontally after passing the boundaries.
and it goes on to say:
g) For the purposes of this section the terms, takeoff distance, takeoff run, net takeoff flight path and takeoff path have the same meanings as set forth in the rules under which the airplane was certificated.
Part 25 contains those rules and defines Takeoff Path as (again among other things):
(2) The airplane must be accelerated on the ground to VEF, at which point the critical engine must be made inoperative and remain inoperative for the rest of the takeoff;
The other CFRs quoted have similar language.
Just beacuse the AC states SIDs assume all engines operating doesn't alleviate the basics. If there is a reverse print "T" on the plate then there is an Obstacle Departure Procedure (ODP) for that airport and you should look it up in the front and comply with it one engine inoperative for commercial operations. If there's none then a minimum of 200 FT/Nm is required, 3.3%, again one engine inoperative. The AC itself states in the begining:
This AC need not serve as the sole basis for determining whether an obstacle analysis program meets the intent of the regulations.
Why we use one engine inoperatve versus say the gear remaining down? Arbitrary. Ironically I've had the gear stay down on me three times but have never lost an engine below 1000'. But that's the way it is.