Dr. Dlugokencky wrote me that the information is at the bottom of the document: the right place to look at is at point 7.6
I had falsely looked under hourly averages.

7.6 DATA - MONTHLY AVERAGES

Data files are located in "/ccg/ch4/in-situ/[site]/". There is one
monthly mean data file for each site, (e.g., ch4_mlo_surface-insitu_1_ccgg_month.txt).
Monthly means are calculated using values extracted at one-day
timesteps from a smooth curve (Thoning et al., 1989) fitted to the daily
averages.

The data files contain multiple lines of header information followed
by one line for each available month.

Fields are defined as follows:

Field 1: [SITE CODE] The three-character sampling location code (see above).

Field 2: [YEAR] The sample collection date and time in UTC.
Field 3: [MONTH]

Field 4: [MEAN VALUE] Dry air mole fraction.
Missing values are denoted by -999.99[9].

Field 5: [STANDARD DEVIATION] The standard deviation is of the mean of
the residuals about the smooth curve.

Field 6: [# OF DAYS] The number of daily averages available.

Field 7: [QC FLAG] A three-character field indicating the results of our
data rejection and selection process, described in section 7.4.

Fields in each line are delimited by whitespace.


Apart from this he wrote that the fraction for CH4 is actually nanomole/mole, whereas if I recall correctly the CO2 was measured in micromole/mole.
I find this information would be also a useful item in the explanation, even if probably a lot of researchers know which CH4 concentrations to expect. But may be I oversaw this and it was mentioned somewhere.