Items and enhancements are supposed to stack, But I think that PM is broken and is not applying the bonus at least at Tier 3.
look at necrotic ray in my case:
My PM 3
Necrotic ray 1d8/caster lvl max 25
45% neg damage from PM3
50% sup potency 6
100% maximize
50% empower
Polar ray 1d6/caster lvl max 25
40% elemental damage Enhance
50% sup glaciation 8
100% maximize
50% empower
Now my necrotic rays are hitting for about 1/3 less damage than my polar rays.
All my other buffs for necrotic ray are working, max,emp, and item.
The description for it used to be 1d8 per caster lvl max level 10, so I went to the PvP pit and had someone enervate me to level 10... nope damage for sure goes down not quite half.
I've submitted a bug report, but I suggest you test it for yourself and do your own tests, then please you submit a report also, I really would like this fixed. And for PM 3s necrotic ray SHOULD be awesome.