What exactly are you referring to as “%Total Damage Bonus”?
Assuming you means “Total Damage Modified by xx%”?
Total Damage Modified by xx% increase the skill damage before conversion, well even if it did after conversion the result would still be the same, because it’s a multiplicative modifier.
So let take an example, the skill deal 100 physical damage and its transmuter gives Total Damage Modified by 100%, the skill now deals 200 physical damage, then if you have 10% physical damage converted to elemental, the skill will deals 180 physical damage and 20 elemental damage.