Roof metal fabricator will sell you foam inserts the match the bottom wrungs or that matchs the "hats" or voids of the metal deck.
Your'll need to match the flutes, the rises and the runs
Most cases the Deck names are , "B", F" and "S";
"B" is 2" in depth or greater, this includes composite that has concrete poured on it.
"F" is 1 1/2" to 2" and nearly matches the flutes spread of the "B" deck, except for the shallow aspect of the void.
"S" Deck looks Like a A/C Sine wave, and can also have concrete on it...
So what do You have?
If most cases these are all Factory Mutual Listings, it's just a piece of standard Foam there is no fire rating to it. they will sell you all of it.
Barring Building Codes, I'd use the foam inserts, use gauge metal and just move the foam back and fill it with fire stop or concrete. I don't believe there is a UL or NEC Code.
Maybe a submittial is in order on you part, draft a matching gauge of sheet metal with a 2 1/16" insert, hole and enough sheet metal to land on you flutes(the bottom wrungs... pack it from two sides, and show a bead of fire chaulk as to where it will land on flutes... Tech 11 screws...
Now, having said all that, it comes down to what is the roofing material and most pentitrations cost dearly, IE no care is ever given to the bottom side (under side) of a roof deck! Just keep that in mind as U ramble through the spec's.
Good Luck...