I'm a government employee, an enforcer of rules and regulations, but not these rules and regulations. However, I do have considerable experience in reading, interpreting and applying gov't regulations.
First the caveat. I am not an expert on BATF regulations and I'm not a lawyer and I haven't stayed at Holiday Inn Express recently, - but - I can tell you this, regulatory enforcement people can and do make mistakes regarding the inpretation of regulations. Even agencies that are charged with the responsibility to create regulations from legislation can get it wrong. That is what the courts are for.
That being said:
My take on reading the posted BATF regulations is that the mfg of the action with a serial # clearly needs a mfg license. Any gunsmith/company buying the action from the mfg and using it to build a rifle for sale to a customer is also a mfg and needs the mfg license. If a customer buys a custom action from an FFL and gives it to a gunsmith to add a barrel, trigger, stock etc. this is not mfg and does not need a mfg license. My interpretation is that a mfg can sell the action (considered the firearm) to you and have it sent to an FFL (that may or may not have a mfg license) to do the paperwork. The FFL dealer in essence sells you the action. You can then give the action to an FFL gunsmith to add the barrel, stock, trigger etc and this would not be considered mfg per paragraph 5.
This is how I read the regulation, as it was presented here. If I was given the regulations, as presented here, and asked to enforce it - that is how I would interpret it. Someone else could read it and decide otherwise. This type of stuff happens all the time. Inspectors in my agency have disagreements on the interpretation/enforcement of regulations all the time. Most of the time the Agency chimes in with the "official interpretation" and sometimes even they get it wrong too. Again, that is what the courts are for.
As I read it, the gunsmiths that might get into trouble here are the ones making spec guns for sale. If the gunsmith is buying the action from the action Mfg., adds the barrel, stock, trigger etc to the action and then sells the assembled firearm, that seems to me to meet the definition of manufacture, unless it was a one time event. Anyone routinely selling spec rifles or adding components on an action that the smith has purchased and is reselling, would be mfg.
If you are a mfg or gunsmith being visited by the BATF and facing this issue, there is nothing wrong with politely saying to the agent "As I read it, I'm not a mfg because I'm not buying the action, my customer is buying the action and I am just adding the barrel and stock and, as indicated in paragraph 5, this does not qualify as manufacturing." If the agent disagrees and especially if they can not explain clearly why your interpretation is wrong, direct him/her to your lawyer. You don't have to just roll over and accept a verbal interpreation presented to you by an agent, inspector, or regulator. Ask for an official interpretation in writing and then give that to your attorney for review.
An agency's interpretation can be wrong and courts overturn these interpretations all the time. Professional organizations are oft times the best ones to handle these issues. Has the mfg in question contacted the National Shooting Sports Federation (NSSF) or the NRA? If not, they should do so.