In the case of Wish, that is not correct. Wish specifically says you must spend the XP in the description. This is why often, you'll see things noted in modules like "So and So has X number of XP for casting Wish spells." There is no difference between a spell-like ability and casting a spell as far as all the other mechanics of the game are concerned.
Spell-Like: Spell-like abilities are magical and work just like spells (though they are not spells and so have no verbal, somatic, material, focus, or XP components). They go away in an antimagic field and are subject to spell resistance if the spell the ability resembles or duplicates would be subject to spell resistance.
Animate Dead specifically says you must place an onyx in the corpse's mouth in the spell description. But if you're using Animate Dead as a spell-like ability, it has no material component.
Enervation specifically says you point your finger and utter an incantation. But if you're using Enervation as a spell-like ability, it has no somatic or verbal components.
Gate specifically states that the 'calling creatures' function of the spell has an XP cost. But if you're using Gate as a spell-like ability, it has no XP component.
Nystul's Magic Aura specifically notes that the small square of silk must be passed over the object you're casting the spell on. But if you're using Magic Aura as a spell-like ability, it has no Focus component.
There is certainly a difference between a spell-like ability and casting a spell as far as "all the other mechanics of the game" are concerned.
If, for some reason, you find the Monster Manual quote unconvincing, consider the description of the Summoning subschool:
A summoned creature cannot use any innate summoning abilities it may have, and it refuses to cast any spells that would cost it XP, or to use any spell-like abilities that would cost XP if they were spells.
Notice that spells have XP costs, whereas SLAs would cost XP if they were spells. Since they're SLAs, however, they don't.