Someone want to explain how the ammeter showing + (charging) somehow means it is low on output?

If it showed - (discharging) then yeah.

Do you have anything else being powered directly from the battery, such as an electric fuel pump?

Fluctuations means it's cycling the charge to the battery, assuming there is nothing wired to the battery non-stock.

They say there are no such thing as a stupid question.
They say there is always the exception that proves the rule.
Don't be the exception.