It's... not expensive at all? Companies don't do their own investigations. The FBI does them, and they charge the same rate for everyone. If the clearance application fee is what's going to break your company, you've got some bigger problems.

I've worked for several DoD contractors. The question on the job application is "is there anything that would prevent you from obtaining a clearance?" It's not "are you a citizen or green card holder?"

And all that doesn't even really matter. Export controlled information is Controlled, Unclassified Information (CUI). It's one of the lowest grades of information we handle. It's in the name, you don't need a clearance to have access to it. Thus you don't need an investigation. The most you need is a background check, which most companies do for everyone, anyway.