If you look carefully at the icons for the abilities, 1 and 3, are not the same color as 2 and 4.  These 2 with the darker colored icons are "improved" and thus have better damage associated.  If you collect a lot of archeotech blueprints, you'll notice that there will be multiple copies of the same item listed for you to craft.  Sometimes they have a different relic enchant, other times they resemble the exact scenario you have here, where they have the same enchant, with differing damages.

In my experience you might find one or two enhanced abilities on any given archeotech weapon.  It's a subtle thing they offered for extensive farming, but like most of the way they explain this game, tooltips, and end game content; much was left to be desired.