I’m fairly certain of this. At least, if I’m recalling some of the testing I did ages ago.
Where it gets tricky is that some nodes in skill lines are treated as an independent damage source (e.g. explosive strike, soulfire, nightfall).
What this means is that transmuter level conversions (aka, skill modifiers) will NOT affect them.
A good example would be EoR. Even if scythe of tenebris might read ‘100% physical converted to chaos to EoR,’ the physical damage on soulfire itself will remain unconverted.
Global conversions matter in these cases.