The horse does not get tired. It doesn't necessarily mean that YOU don't get tired. You're still going be bouncing up and down (unless you've ALSO fused with the horse). You still have to guide the horse (more so, in this case, because your horse can't think). You have to stay ON the horse. It won't try to throw you, but it's still moving very fast. It's not just dragging you along in a carriage, so why wouldn't you get saddle-sore?
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.
Best Answer
Ultimately, it seems that there's little that a creature can do to prevent its corpse from being the subject of a spell like animate dead. However, a creature can prevent itself from becoming an undead spawn upon its death at the hands or fangs of an undead creature like a shadow or vampire.
See the spell spawn ward…
In addition to other effects, the spell spawn ward makes it so the spell's subject "cannot be made into undead spawn if killed while the spell is in effect." It's a 5th-level cleric and inquisitor spell largely because of its other effects, the inability to be turned into a undead spawn if slain while the spell's duration continues appearing to be the spell's most minor boon. However, the spell spawn ward does not prevent a necromancer from using the protected creature's corpse to create an undead via a spell like animate dead.
The spell sanctify corpse can be cast on a corpse to, for 1 day, delay the corpse from rising as an undead and, for the same duration, prevent folks from using the corpse to create an undead creature from it like with the spell animate dead. The spell must be cast on the corpse each day for this delay and prevention to continue. The spell sanctify corpse is a 1st-level spell on many casters' spell lists.
(The spell gentle repose is actually of no help here, doing nothing to prevent the subject corpse from spawning as an undead or being transformed into an undead. The spell gentle repose just keeps a corpse from rotting. There also doesn't seem to be a lower-level spell that grants similar protection to spawn ward like the Dungeons and Dragons 3.5 2nd-level Sor/Wiz spell spawn screen [necro] (Spell Compendium 197), but I doubt a truly vindictive GM that's intent upon turning a PC into an undead creature will allow importing that spell from Pathfinder's antecedent!)
…But, instead, wear a ring of the faithful dead
If all that's sought is not to turn into an undead spawn, the ring says, in part, that if the wearer
The ring is a bargain at 500 gp. The elysian shield has a similar effect among its other effect, but at a much higher price at over 50,000 gp (and the necessity of bearing a tower shield).