Mazila, I'm having some confusion with what you're saying. Are you saying that the rule as written does or should affect both attacking and defending ships?
Nate, I believe your clarification about BMs and boarding modifiers is confusing. Either you're misinterpreting the current rule (probably due to Mazila's input) or you've changed the current rule, which I don't think is necessary.
The rule as written plays that if a ship has a BM in contact, the enemy ship gets +1 to their dice roll. This does not need to be changed to affect only the defending ship. If the attacker has a BM in contact then the defender should get the bonus.
However, there is no rule that says that a ship touching another ship with a BM in contact itself counts as having a BM in contact. This little bit of absurdity is Mazila's input. So, if you don't physically have a BM touching your ships base, you don't give the enemy +1 to their boarding roll. If you do, you do. It's that simple.