@Kimberly Did you solve your problem? I'm also struggling with initial gpio mode and state.
Is it possible to easily set those settings without modifications of script.bin or dtb file? In my case my Banana Pro controls light relays and after, eg. power outage the gpio's gets default settings, which leads to incorrect relays state. Currently I'm storing gpio state and mode in some file and restore it on boot in rc.local, but it is not the best solution since invalid relay state persist for about 1 minute (until boot process reach rc.local script). This is really annoying especially in the night when eg. at 2:00 AM, lights in my bedroom turns on