we aren't sure if there is a way to still use the same Application ID and SKUs defined for our main app when trying to purchase something related only to the SDK part of the code
This would not work because each app would need to have a different package name (application id), a different API key, and would be signed with a different keystore. The in-app items would need to be setup for each app and you wouldn't have control of pricing. You should consider a different monetization strategy.