After a quick comparison of several Wiki pages mentioning Tortodrones or Tortomegas, I have a hypothesis as to the difference and their relation:
I hypothesize that Tortomegas were the original, organic creatures resembling giant bipedal tortoises living in the Clockworks. The Tortomegas were the ancient civilization the Strangers know very little about and mention occasionally. As more worlds and creatures were incorporated into the Clockworks, it became clear their time was limited. They constructed the Tortodrones to essentially replace themselves and fill their ecological niche, knowing they would soon be extinct. The exact nature of their demise is as of yet unknown. The Megas programmed the Drones to mimic their own traditions and functions, including their migration patterns. I speculate this was done in an effort to tell their story. Fiends found these huge constructs, corrupting and hacking them for their own use long after the Megas were gone.
Regarding Torto-related gear, the descriptions for Gorgofist, Gorgomega, and Omega Shell all refer to the Megas.
The Gorgofist and Gorgomega have properties related to Shadow damage or resistance.
Fiends and undead both inflict and resist shadow damage. Megas are extinct, making them closest to Undead in nature.
TL;DR – Tortomega = OG turtle. Tortodrone = Robo turtle.
Megas built Drones. Megas died out. Fiends hacked Drones.
Thinking about it, the Tortodrones could be fully artificial defense and security constructs, or mechanical proxies with minds of the original Tortomegas uploaded into them.
The Eye sigil found on Tortodrone shells shows up a lot on major objects and entities and such in the Clockworks, like the Swarm, heavy statues, a bunch of other places I forgot, and the Sealed Sword and Vortex Bomb lines, both of which have conveniently mysterious origins and incorporate either black-box technology or literal magic in their design.