I cannot find these caps on the SRD, but I know they exist, else a Rod of Undead Mastery and the secondary effect of a Dread Necromancer's Undead Mastery would be useless. Where can I find what the default HD control caps are?
Corpsecrafter et al. each apply to “undead you raise or create with any necromancy spell.” The Ritual of Crucimigration does not involve any spellcasting, only cursed nails, chanting, and the invocation of “evil powers and gods.” It is these things, rather than the ritual leader him- or herself, that result in the creation of the necropolitan. The ritual leader is just ensuring the proper timing of everything. Therefore, the feats that the ritual leader does or does not have do not apply, and again, since no spell was cast, Corpsecraft et al. wouldn’t anyway.
This was likely written this way specifically to avoid players easily getting substantial benefits at no cost to themselves.
On the other hand, desecrate does not have any such provisions. This implies that a necropolitan could gain the +1 or +2 HP/HD that desecrate offers to every “undead creature created within or summoned into such an area.” However, there is no indication that this is a permanent bonus: it is an effect of the spell. Once the spell expires, or the necropolitan leaves the area, the benefit is lost.
Necropolitan is a fairly high-power template. The benefits of the undead type are considerable. The costs are fairly considerable as well, but it is well worth considering for many characters, and dread necromancers benefit particularly well from it. That’s all fine, but piling extra bonuses on top, such as Corpsecrafter or desecrate, that cost you nothing, as they are aspects of whoever performs the ritual, that pushes the template beyond what I would consider acceptable. If I allowed a player to use these, I’d feel the need to offer ways to empower the other characters as well.
Which, of course, can be done and can be quite fun, but it’s definitely not an automatic part of necropolitan.
As GM, you always have more options than you think, and you should always try to choose the one that's the most fun. My vote would be for the following:
4. This infuses the tarrasque with negative energy, creating an eldritch horror that threatens all of existence.
The rules don't say exactly where the tarrasque came from or how it works, but it's safe to assume that the creature is powered by some unlimited source of magic energy deep within its hulking form. The animate dead spell will corrupt this power source with negative energy, creating a threat to existence itself.
The most immediate effect will be the creation of an undead creature much more powerful than the original tarrasque, and certainly not under the control of the PC necromancer. The power of this creature will only grow over time as its power source becomes more corrupt. The creature will emit a negative energy aura that extends for miles, granting many permanent negative levels to creatures who fail their save and transforming most living creatures in the area to undead. As the creature's power grows, nightshades will begin to come forth from the negative energy plane to join with it, and it will begin to emit waves of negative energy of increasing radius. All natural healing of living creatures will cease, the dead will begin to rise from their graves, and material plane will begin to merge with the plane of negative energy.
It's up to the PCs to find out where the original tarrasque came from and how they can undo the damage that they have done. They might also have to deal with powerful planar beings who would use the abomination for their own ends, or who hope to defend the multiverse from the threat now posed by the material plane.