How have you all handled the allocation of indirect material costs to the manufacturing process? Example: we have an assembly that requires glue to adhere components but we do not want to add glue as a component on the BOM as a stand-alone item.

why not add the glue to the bom?

If you have WIP and routings you can add it as part of the mfg cost template but I agree with @Pete Kastner just make it a non inventory item in the BOM

Mostly companies don't make part of BOM, make it non-inventory item, as there cost is very minimal and we can't measure the quantity to be used.

You can use quantity of 0.00001 that was it is accounted for and in a very minimal quantity/amount