While you can't format a USB flash drive under Windows to have multiple partitions, that doesn't stop you from doing so and using one of those partitions in Windows.
You can either format the USB flash drive in Linux or with some applications in Windows in a way that you want your Windows accessible partition to be the first one it can recognize in the partition table. Then you can use the remaining to boot Linux.
Well, yeah. That's what i was getting at. This however doesn't bypass the fact that windows doesn't support multiple partitions on a thumb drive. This has nothing to do with wanting to put multiple partitions on a thumb drive in windows.
Here's how the pointless scenario would go. You'd use linux to format multiple partitions on a thumb drive just to not be able to use all of the partitions on the drive in windows when windows computers is what you have to plug into all of the time. This is why i suggested two thumb drives, since still entertaining the idea of one drive really isn't really going to fix the difficult situation.
The main thing about windows and a partitioned thumb drive. Well, okay sure, access the partition you need access to in windows. However when i was messing around with partitioned thumb drives in windows...i thought of this. I had a hard time with windows showing at least the partition that i would want access to in windows when plugged in. It was a 16gb thumb drive setup for live booting. The smaller partition was fat32 where i had bootable linux, the much bigger partition was ntfs. Plugging into windows sometimes i'd get the fat32 or the ntfs partition. I got one or the other, it was inconsistent because microsoft doesn't support partitioned thumb drives. If you could choose one partition over the other on a thumb drive in windows, that would suggest microsoft has some minor support for partitions on thumb drives, or more likely that there was a way to coax windows.
So, i ask, how would you get windows to favor one partition over the other on a thumb drive? If you know a way, then i would to find this handy