I was trying to be nice in my previous response, but now I see you weren't being sarcastic.....
A Notice of Commencement is nothing like a Building Permit. Nobody at that office reviews blueprints to ensure compliance with codes. Notices of Commencement are filed to protect the Owner (person/entity owning the property where work is taking place) and those performing the work (BVCC, General Contractor, Subcontractor).
They're used to track work being done on any "real property" - so that if someone doesn't get paid for their work, there's a record of it taking place, when it started, and what the work entailed (roughly). I don't do work in Florida, so I don't know the specifics, but I don't think you can be "denied" a NoC....but you get in trouble if you don't file one PRIOR to doing the work, because by then the entire purpose of the NoC is moot.
People like to think that Disney has complete autonomy via RCID, but they really don't. While Reedy Creek will issue actual building permits (after reviewing plans and ensuring code compliance) for any work done within their jurisdiction, any third party doing work on Disney property (or any property in Florida) still has to file a Notice of Commencement with the County - both Orange and Osceola. This includes work done on the major roadways, down to a fiber optic cable run 30 feet through the MK tunnels.
And for the record, neither Reedy Creek nor Orange/Osceola Counties are holding up any major development at the parks. If any governmental entity can be "blamed" for slowing the development process, it's the South Florida Water Management District...but they're just making sure that new development doesn't negatively impact the flow of water around the state (hence all the canals and retention/detention ponds on property).
Hope this clears things up.