This notification simply means that items with variants are not included on your current Clover service plan. Shopventory is not able to overwrite Clover's restrictions per the terms of our agreement with Clover.
To enable items with variants you'll simply have to update your service plan with Clover. Here is a step-by-step guide from Clover's help section on how to do that:
That page also has information about what's included in each of Clover's service plans.