ASP.NET Core (HttpSys) Routing works locally but not when deployed

Solved - The full path base must be added to the UrlPrefix and the urlacl registration so

netsh http add urlacl url=https://*:30010/BasePathOfAPI/ user="NT AUTHORITY\NETWORK SERVICE" 

and in addition to this as controllers are in another dll, the assembly must be referenced in the ConfigureServices method:

services.AddMvc().AddApplicationPart(typeof(SystemController).Assembly)

These two fixes made it work