It won't sound paranoid at all, that is one of the main purposes of compounding pharmacies... to make up medications in forms that do not contain ingredients patients are allergic to or want to avoid.
I would imagine that the reason protopic uses petrolatum in their ointment is because ointment stays on better. So you need to find another base that will stay on well. Perhaps the Un-Petroleum Jelly (if you are in the USA)? Unless there is something in the natural oils and waxes that does not interact well with the drug you need. But a good compounding pharmacist should know.