Atlassian Crowd is a separate product and therefore if you wish to use Crowd for SSO, you will need to purchase a Crowd license that is large enough for your user base. Customers in JIRA Service Desk, while free in JIRA Service Desk, will consume a license in Crowd.

A suggestion to to enable both remote Crowd and local authentication in JIRA has been created. Please vote and comment on this issue to communicate your need for a feature such as this JSD-1244

The scenarios is as follows:
Imagine a company has 50 users Crowd, JIRA, confluence plus other apps. All applications are using Crowd SSO. This company purchased 10 agents JSD. When a customer is added, it is created in the JIRA local directory. Since Crowd SSO is enabled, this customer cannot login. This company cannot add customer accounts into Crowd directory as they have not enough seats.