Yes, a single partition can exist on the hard disk portion of a Fusion drive system, and that will be created by BootCamp assistant.
If you had a DIY Fusion drive created with a larger SSD drive, you could create a Windows partition on the SSD, then use the other SSD partition to create your Fusion drive with the hard disk. This gets you the best of both! I usually use a 512GB SSD divided in half for 256GB Windows, and 256GB SSD + hard disk for Fusion drive.