So, I kinda thought your title was misleading.
Because ALL you talk about, is how we keep finding out that our GUESSTIMATES about how much CO2 and CH4 our activities generate, are far to LOW when we actually measure them. That's NOT a "surprise" to anyone who has more than a room temperature IQ.
The BIG question is WHY weren't measuring these emissions ALL ALONG?
Then you say.
"Do we really know how much greenhouse gas we’re putting in the atmosphere?"
Why yes, yes we do.
We measure the actual amount of CO2 in the atmosphere on a DAILY basis. That would be the Keeling Project and the "Keeling Curve".
So, we do KNOW how much CO2 and CH4 there is in the atmosphere.
What you are talking about isn't "How Much?" You are talking about "Where From?"
That's a DIFFERENT question. An important question but not the same as "how much".
If we are ALREADY past the RED LINE. Where the emissions are coming from does not matter.
The ONLY THING that MATTERS is that they STOP NOW. Because the COST of NOT STOPPING IMMEDIATELY is Civilization Collapse so complete that the next cycle won't even remember who we were.
That's how long it will take them to climb back out of the hole we are digging.