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 variations 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?

You can use Stock Sync to do the below method:

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 to match the same SKU. If disabled, it will only update the first variant found.