You can use Shopify's Discount Codes functionality alongside Single SKU bundles, but unfortunately Multiple SKU bundles are incompatible at this time.
This is due to a Shopify limitation - more specifically, this is related to a quirk of the Shopify platform regarding how different systems interact, which we can't change here at Agile. The Multiple SKU Bundle type uses Shopify's Draft Orders functionality - the Single SKU Bundle does not. As soon as the Draft Orders system is used in any given transaction, the Shopify platform will automatically disable the Discount Code bar and only give Discount control to the Draft Order-related system. As such, the Single SKU Bundle type can be used with Discount Codes, but Multiple SKU Bundles cannot. You can see how other Shopify users have also run into this issue with other, non-Agile apps below:
If you would like to apply discounts to your Multiple SKU bundle, we recommend you use the discount functionality we offer in-app.