Currently, the PSE Server Options are stored in the registry for each user, with default values coded into the application. This is a terrible design choice. The connection settings for an entity connecting to either a Data Archive or an Asset Framework system should be applicable for every entity originated from the server/computer. There's no reason to have different settings per-user. Additionally, there is no "supported" option for changing this settings for a gMSA since the recommendation is to use the GUI to create the registry entries.
These settings should be set once per server and configured (ie. file built) on installation of PSE.