There is a workaround. You can simply not add the entries to the services file at all. From at least GUI 7.30 on, it's possible to instead just put the required information directly in the SAPLogon connection info.
To do this, when you set up the connection as a Group/Server Selection, like you normally would for load balancing or using logon groups, in the Message Server field put the hostname with the TCP Port, i.e like "SAPDEV2:3601" instead of just "SAPDEV2". That's all.
You don't have to put anything into the services file.