"I'm thinking of using the detail section of the consolidated 1099-DIV to break out what a box 1a should be for each fund and then report the sum of the exclusion amounts and report that for the consolidated 1099-DIV government exclusion."
is exactly what you need to do. Enter the 1099-DIV as provided and in the questions after you will be asked how much $ of the 1099-DIV Box 1a is US Gov. You have to calculate that total offline based on whatever funds and their respective percentages make up your 1099-DIV.
