Hmm probably nothing architecture wise. It's probably just the fact that fossil is developed by way fewer devs.
From the skim I read of this article it seems both projects arrived at the same solution: support both but make SHA-256 the default.
SHA3-256 != SHA-256
No it’s different. Git supports both but you cannot mix them in a repo. Fossil allows mixing them in a single repo. This is clearly stated in the link.