Hello, Chaos. Not a bad write up. Here are my notes:
For reasons that I don't care to reveal at this stage, my Overmind does not do much of his own genetic manipulation, leaving it to his Cerebrates. If you think this can be reasonably done, I would prefer you edit your creation story to reflect being the pet project of one of the Cerebrates rather then the Overmind himself. If you want to retain your Mercenary status, one of the deceased Overminds, Lokin or Baal, might be best. Over all, though, I like the concept as a combat oriented Overlord as an evolutionary niche.
The increased air range would need to be paid for out of the damage of the air attack. So, as 6 range would cost 8 (5 more points), the dps of the air attack would need to be 83 (5 less points). Otherwise, having multiple weapons for different situations is not a problem, as long as it doesn't get out of hand. Three attacks isn't that bad, and you aren't cheating discounts, so I'll let it slide.
You're abilities are over powered. BEP does way too much damage for it's energy cost and an ability shouldn't really be weighted toward a particular armor type the way an attack is. The same goes for TftD, which, as a passive, shouldn't be doing that kind of damage, especially not when coupled with an essentially free ability. I don't mind Deep Tunnel, I would suggest actually letting us know what the limitation is: either define a range or say it requires creep. The regen is fine, but I'm uncertain on the numbers I should allow there. Let me get back to you.
Your ship just sounds like a Leviathan. Much like every and any Leviathan. Not particularly unique or special in it's capabilities or tactics. OK, you have bio-electricity, but you don't have the Sec score to let that have any mechanical effect. Cool story though, and I like that you are thinking about appropriate zergy tactics.