The original questions sparked a couple thoughts.
First, it looks to me like you're assuming a specific "amount" of weapon yields a specific weapon factor, regardless of what ship it's mounted in. It might be put together differently, or even expressed differently, but it amounts to the same thing. A size 3 ship with a size 2 weapon has the same rating as a size 4 ship with a size 1 weapon because both add up to 5.
Right?
Okay, so if you're assuming each ship rating increment is a power of 10, this means your weapon rating increment must also be a power of 10 to make the math simple.
It follows then, that the defense factor would work out the same - that is, a specific volume of defense system has a specific rating, regardless of what percentage of the hull it takes up, and each factor implies 10 times as much effectiveness and ten times as much volume.
When you pit offense against defense in this system, you can simply subtract defense from offense and use that difference to determine what the result is.
Now, I don't know about you, but to me, if something is 10 times as powerful as something else, I expect it to perform significantly better. A 16 inch shell will play hell with a destroyer 1/10th the displacement of the battleship that fired it, while the destroyer's 5 inch return fire won't often do much to the battleship.
Basically, at this scale, a difference of just 1 is catastrophic to the smaller unit, with little if any possibility of reply. Few if any players will want to be on the wrong end of that stick.
My own preference, instead of the bel scale (1 bel = 1 power of ten) is the decibel (1 bel = 10 decibels = 1 power of 10). Every 10 increments is a power of ten, but each individual increment is 25%. (A further convenience is that a difference of 3 is a doubling.)
Instead of ships sized 1 to 1 million tons being rated 0 to 6, they are now rated 0 to 60. A power difference of 25% is a lot more believable as a survivable fight than a 900% (nine hundred percent) difference.
Of course, you might not like dealing with numbers as large as 60, in which case you can use other scales (such as each factor being a power of 2 or 3), or you could restrict yourself to ships sized between, say, 100 and 5000 tons and divide that into however many increments you want.
But wait, there's more!
In TNE (and similar design systems), they made it pretty clear that the amount of damage you do is usually related to the square root of the power requirement, and by extension, the size of the weapon (and its reactor slice). This means that a weapon is actually HALF as effective per increment... assuming, of course, that defenses don't hold to the same power law (which they usually don't). This also extends the range of factors which are capable of reasonably engaging each other.
At that point, all you have to do is halve the Offense factor before you subtract the Defense factor from it, and you use this number to decide the result of the attack.
Of course, the exact meaning of that number is up to you to decide.
If this has already been discussed, I apologize for not reading the entire thread to find it.