So far Stock Sync does not affect other apps in your store. This is because Stock Sync is a flexible app that allows full customization.
Apps like Quantity Break: It will automatically create price variation for a different price with the same SKU. But those variations will set no track inventory. I would like to know when uploading inventory data, It will just update Sku with setup Shopify track inventory?
Therefore you can set Stock Sync to
"Ignore don’t track inventory variants" - It will ignore updates to variants that tracking is not Shopify.
"Apply the update to variants that have the same product identifier" - it will update multiple variants that found matching with the same SKU. If disabled, it will only update the first variant found.