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When linking already placed Revit Rooms (see Link Placed / New Revit Rooms to Existing dRofus Rooms and Link Placed / New Revit Rooms to Created dRofus Rooms/wiki/spaces/WA/pages/1318359503 and /wiki/spaces/WA/pages/1332416912), the list of available Rooms will be based upon the currently active Option.
When synchronizing (see Synchronize with Revitwindow interface) you can optionally only synchronize Rooms within the primary Option as highlighted below:
If you are wanting to synchronize a different Option, then you will need to make that option the primary Option.
dRofus does not accommodate Revit design options, however you can work around this by, for e.g., creating multiple Projects within the same database representing different "Programming" options.
Also, see: Create or Update Revit Rooms from Linked Revit Model and Create or Update Revit Spaces from Linked Revit Model.