Any model is going to have some things that are exogenous and some that are endogenous. Climate models usually don't try to predict how much carbon people are going to emit but simply say what the response of the climate is to our emissions under various scenarios. So if this methane is man-made they shouldn't be expected to predict it.
But also climate modeling is very hard. Nate Silver had a whole chapter on what climate scientists are up against in his book, The Signal and the Noise. They have to make due with very long feedback cycles and noisy data. We've known since Svante Arrhenius's work in 1895 that more carbon in the atmosphere will tend to lead to warmer temperatures. Since then we've developed complicated models trying to relate air temperature to sea temperature to water vapor in the atmosphere to plant growth and so on. But this is a very hard task. We know that complicated interactions are going on beyond the simple CO2->temperature model because of things like the weird warming pause in the 2000s before temperature roared back up to trend-lines. But so far we haven't been particularly successful at predicting deviations from the simple model.
This is scary because while we lucked into some climate buffering in the 2000s there's also the possibility of positive feedback loops that might get set off. Scientists have several in mind that might exist, they're trying to predict how much warming might set them off, but they really can't be sure when and/or if they might trigger.
One known possible positive feedback loop is methane release from the arctic. This is something of a known unknown, in that we know its possible but know that we don't have very good estimates of when it'll release and how much. Hence the people in the arctic. Hence people like the scientists in the article going up there trying to lessen the scope of the unknown. Given that methane levels are increasing we know something bad is happening. It might just be a burp before things settle again with most arctic methane staying locked away until global temperatures hit 4C over baseline or something. Or it might be about to get Very Bad right now. More research is required.
Thankfully methane only has a half life in the atmosphere before turning into CO2 and water of something like a dozen years so there might be hope of riding out a methane release, and slow releases can be managed. It's not CO2 which also has an a half-life in the air and oceans dues to rock weathering, but that half life is so long it's beyond any planning horizon we might have unless we start geoengineering to speed it up.