Atolm: Excellent technical drawing to be sure. In an alternate Trek universe it is probably a very sound idea set you have in mind.
Personally, I don't like it as an alternate planet killer model. Maybe for the Whale Probe race in ST: IV would be a better fit with what you have in mind.
However, aside from the newly remastered version, I really don't like the other variations of the Doomsday Machine I've seen online either. One version looks really bad; like a cross between a tadpole and a sperm cell, IMHO.
Why don't I like the other variations?
In TOS the Doomsday Machine was an ancient, neutronium armored robot. It had no crew. It was an automated engine of destruction that once unleashed there was no turning it back or stopping it. It was meant to be an analogous to our planets own planet killers; thermonuclear weapons and the Cold War era threat of nuclear war. Game over.
To add crew or other familar features found on human/iod starships really takes away from its awe inspiring alieness of the planet killer and deminishes the fear factor. It may have looked different fresh out of the assembly yard but I don't think it would have been that different. Neutronium is super dense and very tough stuff. Why does its builder have to be presumably humanlike any way? What if its builders were giant, Cthulhu-like entities that built as a disposable fire and forget weapon that happens to be the weapon that keeps on killing?
You have a chance to negotiate with an alien crew but not against a souless automaton. This very concept is what made the Terminator films very frightening.
Wait, wait, wait. What about V'ger?
V'Ger was willing to communicate because it was looking for its creator and the Whale Probe from ST: IV was probably crewed and was looking for Cetaceans to communicate with. It may have looked very different too off the assembly line.
In the 1980s FASA Trek roleplaying game adventure "A Doomsday Like Any Other", FASA explored the idea that a second Doomsday Machine that had a small crew area AND an external remote control type artifact. As much as I loved that RPG adventure, I still felt that it was dimished to yet another superweapon to be fought over by the Federation and the Rhihannsu.
But what about the other extragalactic races? Tholians are a canon race and I don't recall any canon evidence supporting SFB's idea they aren't from our galaxy. No Tholian superweapons on screen were ever mentioned to my knowledge either. The Andromedans? SFB is not canon BUT even SFB recognized the fear factor involved in having ships that may only be crewed by emotionless automatatons LONG before the TNG introduced us to the Borg. I also don't recall reading anything where Andromedans ships had ever been captured during a battle as the power absorption panels turned beaming parties into extra energy for those panels. That is scary! The canon TOS Andromedans, again weren't souless automatatons and could be negotiated with.
Back to the Doomsday Machine.
IIRC the orginal planet killer drifted into the gravitational pull of a nearby star before TOS science ships could arrive to examine it.
Qapla!
KF