Currently only token logos are supported in the custom network API. Native coins are left with a blank circle instead of their logo despite proper config and image file.
Right now the main option such a project has for getting their basic logo into MM is to request inclusion in the official “popular networks”. However, approval can be challenging for most, and it’s often seen as a political matter. Mostly the MM team recommends relying on custom network API (“for now”) which doesn’t support native coin logos, or to “fork the repo if it’s that big of a deal”.
Properly enable custom networks (native coin) to have logo in MetaMask without having to be included in the official “popular networks” list. This should help reduce the number of requests coming in for inclusion in the popular networks list. A lot of groups just want their own logo visible to their end users when they’re on the network, that’s all.