Same problem. All of my products with variants have item_group_id values, so they should be grouping. Did YouTube’s Merch Shelf stop respecting the group-id recently?
For assistance on Youtube formats their products on their channel, I would recommend reaching out to them directly for more information. From within their app, you can select the “Get Support” option in the channel - When “Get Support” is selected it will bring you to a contact form that goes directly to Google Support.
If there is anything else I can help you with, please let me know.