Update....
The D2 negative carriers fit perfectly, if you have the negative stage plate (
http://store.khbphotografix.com/Negative-Stage-Plate-for-LPL-and-Saunders-LPL-4x5-Enlargers.html). In fact, this plate even has screw holes where you can add studs that match the notches on the back of Omega D negative carriers (though if you do that, then the native LPL holders don't quite fit in all the way).
The negative stage plate also accounts for the difference in thickness I mentioned above: with the plate installed, there is no need for felt, as the Omega D carriers are the exact same thickness as the native LPL carriers.
In fact, I noticed that some of my D2 carriers even have extra bits of metal attached to one face (a flat square with truncated corners) that happens to lock perfectly into the negative stage plate.