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. 

For example:

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 are found matching with the same SKU. If disabled, it will only update the first variant found.