I tried using a fat32 storage partition a few years ago on OE. I can't remember the details but it initially all looked good but quickly turned to poop.
On the other hand I've used Fat32 for 'system' on pc's for years in OE and LE with no discernible issues.
I think if you use NTFS you shouldn't have any issues.
I don't have any Windows - except those I look out of.