In the quantities that honey is typically used, changing the variety of honey will have a slight effect on flavor and aroma, but little else. Strained honey or raw honey might add a slight haze from pollen, but honeycomb, wax, and anything else should settle out during primary or secondary. Ultrafiltered honey should have no effect on clarity. Ultrasonicated honey will be more fermentable and have no wild yeast - so it will dry the beer and reduce the body more than non-ultrasonicated honey.
The extent to which the flavor and aroma will also vary depending on when the honey is added. Honey added during the boil will vary less than post-boil additions, as aromatics will be lost in the boil, and the honey will caramelize. Additionally, hydroxymethylfurfural will form in boiled honey.