Antipitas, all you say it true. But --
Yes, if you are being charged with violating 922(g)(3) and being an user of marijuana in possession of a gun, or with lying on the 4473 by denying being an unlawful user of a controlled substance, the government will need to prove beyond a reasonable doubt that you are a user.
However, as you pointed out, we're not talking about conviction of a crime. We're talking about denial of the transfer of a firearm. That, in and of itself, doesn't result in criminal liability, so a court could find that a different standard of proof applies for the administrative act of declining to authorize a transfer of a firearm (compared with the judicial act of convicting someone of a felony and sending him to prison).
The thing is that we don't know yet what that standard of proof is. It looks like we know what the government thinks it is, and the government seems to be taking the position that possession of a medical marijuana card raises a [rebuttable] presumption that one is a user. We don't yet know if a court will agree.
But something similar happens all the time. We regularly read of folks getting transfers denied for a variety of administrative reasons, e. g., the transferee's name is similar to that of a person with a disqualifying record, or there are errors in the transferee's records. And when such things happen, it becomes the denied transferee's burden to pursue the NICS appeal process and get things sorted out.
I don't know if the NICS appeal process has been tested in court and found to satisfy due process. But it appears to still be in routine use.