It actually increases their hit points, it is permanent.
Does that mean that the other bonuses are also permanent? If not, why is one but not the other?
Because it states that is what happens:
This spell imbues an area with negative energy. The DC to resist negative channeled energy within this area gains a +3 profane bonus. Every undead creature entering a desecrated area gains a +1 profane bonus on all attack rolls, damage rolls, and saving throws. An undead creature created within or summoned into such an area gains +1 hit points per HD.
If the desecrated area contains an altar, shrine, or other permanent fixture dedicated to your deity or aligned higher power, the modifiers given above are doubled (+6 profane bonus to negative channeled energy DCs, +2 profane bonus and +2 hit points per HD for undead created in the area).
Furthermore, anyone who casts animate dead within this area may create as many as double the normal amount of undead (that is, 4 HD per caster level rather than 2 HD per caster level).
The other abilities are conditional on being in the area. Hit points are not gained when they go into the area, only if "created" or "summoned" into the area. You have two beneficial statements with totally different clauses/triggers.