Exhaust note and engine sounds have a huge number of reasons why they are different. Fundamentally, there can simply be firing order. Harley has a single pin crank that creates an odd firing sequence (degrees of the crank), they even tried to patent the sound! Intake & exhaust port placement in the cylinder head, valve overlap and valve duration factor into the sound. The cylindrical volume of the engine, ratio of cylinder diameter to swept area and piston speed affect sound. Resonant tuning will affect how the engine sounds in certain rpm ranges. Double wall and single wall header pipes, pipe diameter and how the pipe is anchored at each end matter. Balancing pipes between cylinders, common exhaust plenums, 4 into 1 into two; 4 into two; 4 into two, into 1 type arrangements. Mufflers can have all kinds of different packing and acoustical baffling. Recently cats get into the mix in different flow styles and locations. Mechanically, there are different flywheel effects, number and style of balance shafts (if any), various chains within the engine and internal gear drives. As mentioned previously, the gears can be square cut, bevel, Hypoid, worm, helical, ring & pinion, 'Quiet', and a huge number of ways to cut each of these styles of gears.
It would be hard to make two engines of different design sound the same unless you strangled the life out of it with serious mufflers and block damping.
I took my moderate sounding V-Max and jetted it up, added an aftermarket exhaust and an adjustable spark timing unit. Afterward the engine rumbled and ripped just like a small block Chevy, I couldn't keep my brother from starting the engine and revving it just to hear the sound.
