You can blacklist a Shopify location in the app. Duplicate SKU inventory on the blacklisted locations will not be synced.
Consider you have 3 locations A, B, and C. Say, you want to sync duplicate SKUs on locations A and B only - leaving out location C. You simply have to add location C to the blacklist. The app will simply stop syncing SKUs on location C.
Once a location is added to the blacklist, the app will disable updating quantity via quick view and detail view pages.