First off no its not Site enabled its per site.
Why would it be a problem there? It doesn’t provide a feature that’s it.
But if I go to a subsites login page and login, then I expect to go to that subsite. If I click Home on the subsites pages I expect to go to the subsites home.
To me this is an issue with either wordpress not linking to the subsite home and linking to the network home instead, or its a problem iwth domain mapping. If the Custom Admin Branding offered a way to change the link and it was doing this then yes I would say there is a problem with it.
Barring any other reasonable solution, is there a custom branding plugin that allows me to change the link on a per subsite basis?