[3.5] The Rogue Handbook: A Fistful of d6

[ShneekeyTheLost]

That doesn't make any sense. These are different types of abilities, with different rules.
The Darkness invocation simulates the Darkness spell, but it's always a SLA rather than a spell.

And the feats explicitly work with Darkness as a spell-like ability, because they function with, and use charges of, and in fact has the prerequisite of, the Darkness spell-like ability, most commonly mentioned being the racial ability of Drow. If it didn't work with SLA's, then they would be completely worthless.

furthermore, it explicitly states in the description of the invocation "Use Darkness as the Spell".

So yes. It works.