The relevant documentation for this is here: https://learn.microsoft.com/en-us/azure/active-directory/app-provisioning/how-provisioning-works#de-provisioning
Upon review, these docs appear to be a bit unclear - we'll work on making them clearer. The behavior that you're seeing is expected. For the custom non-gallery SCIM application, as well as most of our SCIM gallery integrations, we'll only disable users in the connected SCIM application except for when the user has been observed as being hard deleted from AAD. This is not customizable. We are looking at expanding the amount of control that customers have over what happens in these scenarios so that certain conditions can be set to lead to either a disable or a delete. We do not have an ETA that can be shared at this time regarding when those changes may come, however.