Yeah I have wrestled with the collision rules too. I think it comes down to whether you want to lean towards a heavy damage ramming influence, ala Greek and Roman battles, or more of a cannon ball boarding influence. I decided on the cannon ball boarding influence as I truly think, even with the pirates, ramming other ships was a stupid thing to do. With the exception of fire ships, which isn't simulated in this game. I like the battles with the cannons and the boarding action as something more akin to reality for that time.

So I use someone's adjusted rules, which is compare burden's of the ships, subtract the difference and that difference is the damage done to the lower burden ship, but as a minimum each ship will get at least 1 damage counter, even if the burdens are the same. I found this works best for my influence.