"2. The contractor placed an "off brand" ice and water shield as an underlayment ( I asked for the ice and water shield but I was thinking grace...)."

I am not aware of any roofing underlayment that is made by Grace that is vapor permeable so it is unclear if you wanted the underlayment to be vapor permeable or not.

What is the thickness of foam in the roof and where is it placed, tight to the sheathing or not?

If condensation occurs in some [yet to be described] space in the roofing system where would the moisture come from and what would cause a surface to be cool enough to create condensation?

If the climate is hot you might need to consider an underlayment designed for high temperatures.

I'm not sure why a granular surface would harm a metal roof system. What kind of metal is it? It might make some noise when the sun rises and falls. It's hard to imagine how the building felt could cause any harm and it's cheap.

Thank you for the response,

I was thinking that the grace underlayments would be permeable, but apparently they are not.

The foam will be placed under the plywood ( thickness to be determined by the GC).

During the summer the outside temp gets to 110F+ but the attic temp should be similar to the a/c room temps (+ 5~10 degrees?). The temp difference between the hot outside and cooled inside attic space could result in condensation at the plywood level??? The spray foam is an open cell and will allow vapor to go through.

The expansion of the metal and the friction to the granular surface could remove the corrosion protection from the metal underside...

I've already asked the manufacturer of the underlayment the reasons for not recommending using it with metal roofs. I specifically asked about the high temp. I'm waiting for an answer.

Have you considered using closed cell foam?