I just watched a short video about gun trucks in Vietnam on the Smithsonian's youtube channel. In the video they describe why and how gun trucks were built and they claim that the M60 was the only machine gun which soldiers were authorized to install on them.
However, soldiers preferred the M2 or the minigun so they found "alternative ways" to obtain them and then these "irregularly" armed gun trucks were used to protect convoys driving around the country.
I assume a high number of Army officers must have seen these gun trucks and that these officers were aware of the regulations regarding M2s and miniguns.
How come these gun trucks were still allowed to exist? Were there any consequences for using unauthorized weapons in this particular situation? And in general?
The officers were the ones leading the development of the Vietnam era gun trucks. Company, Battalion, and Group (Brigade equivalent) level transportation officers in Vietnam were heavily involved in these field modifications, and they also were the ones creating the doctrine to allow their units to use these gun trucks as effectively as possible. Not only that, many of them recorded their experiences to share and preserve the lessons learned and at least one Captain went through the effort to have a gun truck sent to the US Army Transportation Corps Museum to serve as an example for future generations. So this wasn't a dirty little secret the soldiers tried to keep to themselves, it was leadership pushing this as a reaction to the conditions in Vietnam (along with other tactics to protect convoys).
Now when they say "authorized", they're referring to what's listed on the official Army "TO&E" (Table of Organization and Equipment) for that type of unit.
A TO&E is a document that lays out the organization and weapons/vehicles/equipment for a given type of unit according to Army doctrine. Everything from how many soldiers they're supposed to have and how the unit is organized, to what type of weapons each individual soldier is assigned, to the types and numbers of vehicles used, what (if any) weapons are assigned to those vehicles, and so on. If something isn't on the TO&E, the Army isn't going to issue it to your unit, hence the backdoor deals to get added weapons in Vietnam.
While the Army didn't adopt the idea of the gun truck at a higher level (it was never added to the TO&E and mostly forgotten after Vietnam), I'm not aware of anyone getting in trouble for any of these field modifications in Vietnam. While it was not necessarily viewed by everyone as the ideal long term solution to convoy security, it was also not viewed as a problem that needed to be stamped out.
Richard Killblane, a historian for the US Army Transportation Corps (featured in the Smithsonian video you referenced) has written two papers on the history of US Army convoy security.