It should work with Windows 98, but I can't say for certain if it won't have problems.
I recently got Windows 98 running on a H97 motherboard, so the chipset itself isn't usually a problem (you can use the drivers that come with Windows or find a set of Intel chipset drivers). You might have some trouble getting the on-board devices (LAN, HD Audio, Intel Graphics) working with Win98 since drivers from that time period are hard to come by. You might need a Win9x compatible PCI NIC and/or sound card.
You can also run into trouble if you install more than 1GB of RAM. You can install more, but you'll need to limit the RAM in the SYSTEM.INI file or use Rloew's memory patch.
On-board USB should work out of the box. The NUSB drivers will add more USB functionality to Win98.
The good news is that the Radeon x800 PCIe is completely compatible with Win98 when using ATI/AMD's last driver set for Win98. I personally use a Radeon x800 XL for my Win98/Me retro rocket. Great card!