For default, your ntp configuration will use the inet.0 table and any interface available in this table to reach the ntp server. Any source address should belong to the inet.0 table, so cant use routing-instances with a minimal ntp configuration.
If you dont do this, you will get error messages as "address unavailable" or something else. For example, if you try to use a source address that belong to a routing instance, then this will not be present in the inet.0 table and you will get this messages or something like.
If you want to use any source address that belong to a routing-instance, then will have to use rib groups, this way you could leak some of your routing instance interface address to the inet.0 table. And the opposite, the route to the ntp server from the inet.0 table to the routing-instance. I got this working on MX series, not sure if you could do the same in SRX.