ITO does a good job of dividing these expenses. I figure it as a wash. The GC is bringing you work without advertising expense. The GC or homeowner is paying for the permit. The other expenses are overhead.
I can only think of three departments in my limited territory that require registration fees, and one that I pay the license and insurance for. The total of all these Licence, Registration, and Bond fees is less than $1,000 per year.
However, if I'm working in a new area I call the building department and ask the following:
Do you have a Registration Fee?
Do you have a Bond requirement?
What Code are you on and do you have any ammendments?
What do you want to see for a grounding system? (I ask this because the response varies from unprotected conductor to bonded and tagged RMC).
I use this information to formulate the bid, but I'd never show it as a line item or an extra with a Contract Proposal.
Dave