Converting unholy runes won't be any more of a damage increase than converting frost runes.
You can't howling blast with an unholy rune, but you can't howling blast with an empty frost rune either. Converting unholy runes isn't making them any more useful overall, you will still end up with a rune you can't spend on howling blast roughly every 9 seconds regardless of how many times you have blood tapped your unholy runes.
Honestly I don't know why blood tap sims better in patchwerk conditions, it just does. Apart from the fact that it gives you resources non-randomly when you want them there are a couple of real encounter advantages that I have mentioned already, but other than that I just don't know.
Going to assume it has something to do with resource capping in high gear levels due to the fact that Frost DW has very very low downtime even in low gear levels with full mastery reforges, and that while clearing both Unholy runes is barely a theoretical gain (you clear it "once" per fight, so it's a total of 1 extra rune used in a fight then after that you clear every ~9s) the effect you gain from returning U runes is that during haste trinket procs/bloodlust or even your general play, is that it prevents you from capping out 1 sort of rune by returning one at max stacks while you have D/F runes recharging (since you're aiming to remove that last U rune anyway).
Hope my post was clear enough :/
RIP Breath of Sindragosa - 23/06/2015 - The day fun died.