You can still have a central saplogon.ini file and use the registry key to manage it.
SAP GUI Logon Configuration - Netweaver Technology - SCN Wiki
step 5a.
5. Your users can also use both the server and their own local configuration files together. This can be configured in the following ways:
a. You create the registry key ConfigFileOnServer for your users on their local machines as follows (note that the same key value ConfigFileOnServer under current user HKCU must be deleted if existing):