-"New type" undead like zombies have the interesting effect of blocking bringing the creature back to life, including effects that create you a new body like reincarnation. The only logical explanation is that such undead trap the body's original soul, probably as their eternal energy source. Only by destroying the zombie can that creature come back to life in a new body. And that's why animate dead is Evil while animate objects (just making bodies move) and enervation (negative energy beam ho) are not
That's pretty much what happens indeed. The soul is trapped into the animated body. Though that may not mean that the Zombie, even if awakened and getting a personality of its own, would be using that soul as its own for a potential afterlife.
-Constructs can't be turned into undead indeed. Just like elementals. Even specimens such as a flesh golem can't be zombified despite being perfectly fine flesh, because the original soul is long gone, replaced instead by an elemental soul, and those are no good for necromancy. You simply cannot make a zombie of a being with an elemental soul.
Not necessarily true. A construct, flesh golem included (they actually need a casting of animated dead for the creation), can technically be turned into a zombie. All it needs is a skeletal system as part of its construction. Because apparently that's needed for the zombification process to work. As would any construct with some kind of skeleton (could be one made of metal?)
Even an elemental can be turned into a necromental. Constructs can be turned into undead creature bu many spawn-based undeadifications require the humanoid type.
As for a specific examples, I did mention the animated object and the bogun, who are created with magic as their animating force. Otherwise, the first construct I came upon in the MM4 that isn't mindless is the Clockwork Mender. A construct that builds more of itself on Mechanus and apparently needs something about the plane of Mechanus to start its animation process. It doesn't need some kind of spirit and they still work outside of Mechanus (but don't reproduce). Could be interpreted as them getting a "soul" from Mechanus, I guess, but it is a mystery.
In the regular MM there are the Inevitables that are sentient constructs.
Inevitables are built and programmed in automated factories called creche-forges; one of them, mentioned in the Manual of the Planes, is called Neumannus (a reference to Von Neumann machines). Every type of inevitable is designed to enforce a particular type of universal law and will pursue its objective at any cost. In order to fulfill their tasks, they may ally themselves with other creatures or, if necessary, sacrifice themselves.
After they complete a mission, they go in search of other transgressors, some of whom they may have encountered while on previous missions. Unlike other constructs, they may learn from experience and may even develop individual personalities over time. Eventually, they are called back to Mechanus, where their personalities and knowledge are erased so they can begin anew.
As for the Conscious Android, I thought it could get a bonus Relationship feat toward anyone it already has a relationship feat for. Could get bonus effects depending on the relationship type.
Perhaps it could allow one to take an immediate action to catch the companion's escape pod when the mecha it occupies is destroyed. Can then choose to have him or her join your cockpit.
While using Two with the Machine, could instead choose to have the loved one take your escape pod if your mecha is destroyed while you are piloting it. Since there is normally only one.
If you already have 3 relationship feats for the companion, may work as an effective 4th pick or allow a retrain. Or give the bonus effect for having all feats.
Examples:
Love; Once per round, when the loved one uses an ability that heals you, improves your stats (must not be one you were already benefiting from) or cures you from a negative effect, you heal by 10% of the loved one's maximum hit points.
Friendship; When making a synchro attack, you may make an additional basic attack with a non-heavy weapon and take a -5 penalty on the attack roll.
Rival; Whenever you and your rival are both attacked by the same opponent within the same round, you may roll an opposed level check. At the beginning of his next turn, the winner adds the result to his DR against attacks from that opponent for one turn.
Devotion; If the one you are devoted to is damaged more than once by the same opponent within the same round, you may make one basic attack against that opponent with a non-heavy weapon.
Could also add more uses per hour/day for the relationship feats. Since it already heavily encourages the character to max the relationship feat (and they don't get bonus pilot feats), could keep on making them better at what they do.