>If you are using flash, and have the ISO mode set to "auto ISO" every single time you use flash, it will set the ISO to 3200.
That is not entirely correct. The camera will only select your highest ISO if the meter reading without the flash would have called for that ISO. In other words, it only occurs in low light situations. To demonstrate, set your top AUTO-ISO to 3200 or 6400 and then go outside in bright daylight and take a flash picture, basically a fill-flash picture. Notice that the ISO for that shot is not 3200 or 6400, but rather closer to your preferred setting of 100 or 200.
I haven't verified this since I rarely use the built-in flash, and if I do I turn off Auto-ISO, but I read an explanation that I believe stated that the camera reduces flash output rather than lowering the ISO. Personally, I don't like this firmware decision, but turning off AUTO-ISO or limiting the top setting is an easy workaround.