The augment system from the beginning has been driving people crazy. And while the new iteration is a step up, I feel it is just a needed step to a finalized solution. At this point, it is buggy or seems that way. Augments turn on and off in the blink of an eye, the smallest change. Can't tell what is linked to what unless you inspect it.
And I suspect this method of auto-linking is what drives the build limit to what it is since augments and crafting stations need to scan for each other. This has to stop.
What I suggest is allowing the user to link/unlink and augment themselves through a UI interface. This would not only ensure the user can easily get the augments they want or need at the time, but also stop the wishy washy linking that occurs, and even possibly solve the build limit issue that augments seem to pose.
I have noticed when online they bug more than when offline under 0.5. Relogging syncs them. The green links are gone when moving and I made an item to verify that the item did not get the bonuses (lack of link not cosmetic!). This happens when I move several to change what bonuses apply to a bench, usually workbench and crafting different items. Also, when it desyncs then the green line goes to the wrong bench, aka the beehive showing a green link to smelter or cook bench.