"why can't you collect the gas like air in a column and vent it at the top?"
You can vent any air or other gas that separates from the water. That is the same method that is used to vent air from circulating systems such as hydronic heating systems.
Most gasses will dissolve in water to some degree and will reach equilibrium between the gas pressure and the amount dissolved in the water. That is what happens when methane is mixed with water in the aquifer. When the pressure is reduced, some of the gas is released from solution. If the total pressure of air and gas in a tank is greater than atmospheric pressure, the gas/air mixture can be vented.
The process for removing methane or other gas in single tank systems is to mix the water with air, and vent the resulting mixture of air and methane. Some of the methane is thereby removed. Some of it remains because there is still a partial pressure of methane in the tank, and because there is not enough time to reach equilibrium. Spraying or otherwise mixing the air and water increases the rate of gas exchange and produces a condition nearer equilibrium.
It is virtually impossible to remove all of a gas from water by any practical or economical method. It is only possible to reduce it to very small, usually insignificant, quantities.