Since Mikrotik did great work to support multi-services via VRF, but still #checks-for-update is not supported to use the VRF table instead of the main table,
Anyone had any idea how to force the router to go through the VRF when it needs to go to Mikrotik servers
Until MikroTik update the RouterOS update check function with a VRF selector, you can use this workaround if you really need the update process to go through a different VRF: