Heating honey will not remove the "seed". It will however change the sugars, thus keeping it from granulating.
I would imagine for most on here, seed is not a factor as there is enough seeds regardless of the type of straining. To remove the seed enough to make a difference, you would need to high pressure filter the honey. Anything less and you have seed anyways.
So it really comes down to the sugar makeup of the types of honey, and the temps to which it is stored.