Yes, you can download from multiple folders using one GoogleDriveConnector transformer. However, you will need to know the Object ID for each folder you want to download. These can be obtained using another GoogleDriveConnector, or a hardcoded list attribute. Then you can iterate through those IDs and pass each one to GoogleDriveConnector's Object ID parameter using an attribute.
I checked here in my FME Desktop the transformer and I believe is necessary to use just a Subfolder per transformer.
Thanks,
Danilo