Since OData Web API V5.7, it allows to set a custom namespace for individual function and action in model builder.

Set namespace for function and action in model builder

ODataModelBuilder builder = new ODataModelBuilder();
builder.Namespace = "Default";
builder.ContainerName = "DefaultContainer";
ActionConfiguration action = builder.Action("MyAction");
action.Namespace = "MyNamespace";
FunctionConfiguration function = builder.Function("MyFunction");
function.Namespace = "MyNamespace";

The setting works for ODataConventionModelBuilder as well.