I'm also shooting 143 gr ELD-x (same 6.5mm bore but in a .260 Rem) and I have to seat mine 0.090" beyond the SAAMI maximum overall length measurement to get a "proper" free travel/jump of 0.015"

That's almost 7/8" of exposed bullet ahead of the case mouth! And partially because of that I also check run-out with a concentricity dial indicator. I also found that decapping separately, forming without a deprimer/cherry (I use Redding dies) and then using a K&B Neck expander mandrel in separate steps made working with those copper pencil bullets much more consistent. Though none of those steps would make 1/10th of an inch difference in group size - but the free-travel might make some difference if you're hopping 0.20" instead of 0.02" to get to the rifling.

You also want to make sure you are using a bullet seated insert designed specifically for VLD style bullets.

When you say Factory Loads shoot better are those also with the ELD-x bullet?