So, whats the best and most effective way to use these? I'm 1/3rd of the way through the last tier of def mods so should have it done in a few days.

Destroy all buy one of your Trans-Entropy Drive - Mark III, get it to 100%. Add a second Trans-Entropy Drive - Mark III and get it to 50%.

This way if Dan adds more defense modules, odds are you won't have to upgrade those two modules plus you are getting the best use from the artifact.

Exergonic Inverter - Mark III Defense +626
Trans-Entropy Drive - Mark III Defense +820
Trans-Entropy Drive - Mark III Defense +1640 (100% Upgrade)

I was thinking the exact same thing, thanks so much for confirming for me