Dell typically has proprietary systems with proprietary Motherboards.. Finding an off the shelf replacement will be difficult at best, and more then likely almost impossible.
You will run into this issue with most Major OEM systems (Dell, Compaq, HP, Sony, etc..) All the Dell Desktop systems I have here are closer to a BTX motherboard than an ATX style. The BTX mounts on the opposite side of the Case for one... the Dell Servers I have are all custom for sure, with Riser board for the cards to fit in, etc..
Contact Dell for guidance.
If you build your own system with standard parts, upgrading the system, replacing the motherboard etc.. will be fairly easy.