It is well known that split damage types ultimately boost a weapon's power — something to the effect of the defense formula is run twice, and due to how it works, this causes the amount of damage dealt to be larger (if it was sufficiently large to begin with, which it generally is).

There is a conceptually simple, but technically difficult fix: instead of split damage doing multiple instances of damage added together, apply it as one damage instance with a defense value averaged from weights based on the damage type distribution.

I am going to make a simplified example: let's say that when an attack is neutral to a monster, it deals +25 damage, and when it is effective, it deals +50; and that Leviathan Blade has 100 Normal damage, and Combuster has 50 Normal and 50 Elemental damage.

While Combuster's behaviour is about as expected vs Undead and Constructs (in fact it's really good), it is also performing better against Fiends and Jellies than Leviathan Blade. In this scenario:
Combuster:
(50+50) base + (50+25) defense modifier = 175 total vs Elemental Weak
(50+50) base + (25+25) defense modifier = 150 total vs Elemental Neutral
(50+50) base + (0+25) defense modifier = 125 total vs Elemental Resist
Leviathan Blade:
100 base + 25 defense modifier = 125 total.

The expected behaviour would be that Combuster does the same damage as Leviathan Blade in this situation, which would look more like:
(50+50)+(50*0.5+25*0.5) = 100 base + 37.5 modifier = 137 total vs Elemental Weak
(50+50)+(25*0.5+25*0.5) = 100 base + 25 modifier = 125 total vs Elemental Neutral
(50+50)+(0*0.5+25*0.5) = 100 base + 12.5 modifier = 112 total vs Elemental Resist

Key here is that instead of averaging the defense values, they are weighted based on damage distribution. What this means is that if Combuster instead did 67% Elemental and 33% Normal, say, then that would be reflected in its effectiveness without creeping its normal damage:
(50+50)+(50*0.67+25*0.33) = 100 base + 41.75 modifier = 141 total vs Elemental Weak
(50+50)+(25*0.67+25*0.33) = 100 base + 25 modifier = 125 total vs Elemental Neutral
(50+50)+(0*0.67+25*0.33) = 100 base + 8.25 modifier = 108 total vs Elemental Resist

Again, this example is greatly simplified to make my point. The way SK's defense actually works is something to the effect of a piecewise function that dramatically reduces low attack values and slightly reduces sufficiently large values, and I don't want to dig through forums looking for the research because my point remains the same.

If you didn't know that split damage has a dramatic effect on damage, it's easy to observe: compare Leviathan Blade's 258 hit 3 and Combuster's 292 neutral hit 3. Damage bonus makes the difference more apparent.

The lazier (but more tedious) solution would be to adjust the base damage value and individual attack damage modifiers for split damage weapons so that they line up with expected values for non-split damage. Or remove split damage altogether. But I feel this solution would be best because it balances out split damage without manually adjusting every weapon that currently has it, and opens the opportunity to do more things with split damage.