The cost deferred with program accounting for cost are production cost, nothing else. Not facilities, you activate them and wright them of over many years. Not tooling, like moulds, you again activate them and write them off over many years. A facility has a bookable worth, tooling has a bookable worth.
The cost you defer you would not be able to activate, it is gone, nothing to show. It is the actual cost to produce those 500 first frames, material, salaries, transport cost and so on. You deduct from that the estimated average production cost and the rest you defer.
Boeing and its suppliers can structure their contracts in any way that best suits them. In principal the parties in negotiating the contracts would do so on the basis that they were commercial in nature and minimised risk.
Now I am not too sure about you, but if I was negotiating a contract I would want to make sure costs were properly provisioned through incoming revenues, as this would minimise the risk of a project being a financial drain on the company. We only have to look at the KC46 program where Boeing charged the government a minimal amount for the development of the aircraft and incurred upfront costs. There have been many statements to the market in concern to this.
If we consider the 787 program and Boeing's agreements with its suppliers there would be many elements to a contract. For instance, in many cases the suppliers were responsible for the "development" of the parts they were supplying. As such the contract would have provisioned for this part of the agreement and how costs for "development" would be charged to Boeing.
I'd suggest these costs would have been charged independent of sales and over a set period of time (i.e. progress claims over a 10 year term).
Another part of the contract would have provisioned for "facilities", "tooling" and operational costs for producing parts for the 787. In this instance, there wouldn't be too many suppliers who could finance the development of a greenfield site, including equipment, tooling and overheads for a project where revenues from the sale of parts were delayed for 2-3 years. Again, the agreements Boeing and its suppliers had with each other would have provisioned for such scenarios and how these costs would be paid for if such an event (as it did) occurs.
Another aspect of the agreements Boeing would have with its suppliers is that of Intellectual Property (IP). In some instances the suppliers were licensed to use "IP" owned by Boeing, where in other instances Boeing was licensed to use the "IP" owned by its suppliers. In some instances Boeing had exclusivity rights for "IP" owned by suppliers. As such the agreements Boeing had with its suppliers with regards to "IP" would have been provisioned for in the contract.
Again, the question becomes how "IP" costs were charged to Boeing. It could have been provisioned through a simple percentage of sales (as you assert), a separate IP licensing agreement charge (made independent of sales) or a combination of both.
Your post simply asserts that Boeing has to a treat a cost on the basis of depreciation. The reality is depreciation can be treated many ways and as such should not be used as a guide for how costs should be accounted for in a project environment. For example, my companies manufacturing facility in Australia was able to take advantage of Accelerated Depreciation tax rules when purchasing equipment. This meant we were able to incur higher depreciation costs (reduced taxable incomes), even though the depreciation schedule was not representative of the economic life of the equipment.
Different countries have different tax laws!
In reality all we know is that in 2017 the 787 program has "Deferred" costs of ~$27 billion and that the Boeing board (in their wisdom) continually inform the market about how deferred costs are tracking against a program accounting method.
From this perspective, all we can do is assume costs have been properly provisioned for..........regardless of a logic chain focusing on the basic principles of depreciation.