I feel like HD engines make the power they make by choice, not by limitations of design. There are plenty of guys who can get 100hp or more out of these engines but the reliability starts to suffer. Heck my father's Evo fat boy gets over 100hp on a stock bottom end but it does so by using a roots blower to huff 8psi boost into it. It's literally a cam and a blower and that 1340cc engine is churning somewhere in the 120hp range (it's been a decade since I have looked at the dyno sheet).
The HD engines are aircooled. It's part of the "mystique" but that means they run looser tolerances. most don't run oil coolers either. Ask any aircooled VW guy - when HP goes up, heat goes up, reliability goes down.
Sure ducati was able to pull 100hp out of an aircooled 1000cc engine but it ran a pretty big oil cooler, was OHC, high compression, dual spark, Fuel Injected, and had a cam profile that lugged below 3000rpm. Plenty of drag racers pulled 100hp out of 1000cc ironheads on stock bottom ends by doing the same thing: converting to dual plug, running higher compression, running large oil coolers, head porting, and big carbs. Sputhe built a street legal sportster called the "aluminum steamroller" that was alloy barrels, alloy heads, 1290ccs, and made over 130hp easy (I believe at the rear wheel not at the crank). Still had that same 45 degree angle. So it's possible for HD engines to make comparable power for their size, so why don't they?
rider expectation.
Your average HD sofaglide buyer doesn't want a top end charge. They don't want to feel like they are lugging it below 3000 rpm. They don't want a fast rev and the ability for the engine to quickly change direction. They don't want loading up spark plugs. They want to pull away from a light at 1200rpm and feel like a tractor or a bulldozer is pushing them from behind. They want to punch it WFO at 1500rpms (as soon as they pick their feet up) and don't want it to stumble or cough but effortlessly pull them forward with authority. By the time they make 5K rpm their nuts ran out on them well before the engine breathing did and they back off anyway. They want to lope along in 6th gear on the highway at 2500 rpm and be able to punch it and pass someone.
To that end HD head, flywheel, cam profile, and heck even materials used support a high torque, low HP engine. They are the pickup truck engines of the motorcycle world - durable and understressed.
If you doubt this look at the v-rod. 116hp and 84 ft lbs out of 1131ccs and passes emissions. It's water cooled, reliable, 60 degree twin, and HD people hate it because those things are not "traditional HD". By the way, HD sold a 165hp version of the v-rod called the destroyer - it was a stunningly reliable bracket racer out of the box. Even the later Rods make something closer to 130hp out of 1247ccs.
A the end of the day HD has no incentive to make a high "HP" engine. Their buyers don't want the compromises that comes with a high hp racing v-twin - they want pickup trucks that pull stumps and whip donuts. why mess with what works?