Multiple streams within one rpc / session is ok. A netconf.trace from a quick test using the examples.confd/netconf-notifications/ example, note how I create a subscription to both the built in NETCONF stream and the example interface stream:
$ cat netconf.trace
**> sess:28 new session
3-Nov-2017::09:12:31.581 **< sess:28 write:
<hello xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
<capabilities>
<capability>urn:ietf:params:netconf:base:1.0</capability>
...
</capabilities>
<session-id>28</session-id>
</hello>
3-Nov-2017::09:12:31.591 **> sess:28 read:
<hello xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
<capabilities>
<capability>urn:ietf:params:netconf:base:1.0</capability>
<capability>urn:ietf:params:netconf:base:1.1</capability>
</capabilities>
</hello>
]]>]]>
#389
<rpc message-id="2" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
<create-subscription xmlns="urn:ietf:params:xml:ns:netconf:notification:1.0">
<stream>interface</stream>
</create-subscription>
<create-subscription xmlns="urn:ietf:params:xml:ns:netconf:notification:1.0">
<stream>NETCONF</stream>
</create-subscription>
</rpc>
3-Nov-2017::09:12:35.777 **< sess:28 write:
<rpc-reply message-id="2" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
<ok/>
</rpc-reply>
3-Nov-2017::09:12:47.187 **< sess:28 write:
**> sess:29 new session
<notification xmlns="urn:ietf:params:xml:ns:netconf:notification:1.0">
<eventTime>
...
03T09:12:47.186597+01:00>
</eventTime>
...
<netconf-session-start xmlns="urn:ietf:params:xml:ns:yang:ietf-netconf-notifications">
...
3-Nov-2017::09:12:47.187 **< sess:29 write:
<hello xmlns="urn:ietf:params:xml:ns:netconf:base:1.0"2017-11-
<capabilities>
...
</capabilities>
<session-id>29</session-id>
</hello>
3-Nov-2017::09:12:47.192 **> sess:29 read:
<hello xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
<capabilities>
<capability>urn:ietf:params:netconf:base:1.0</capability>
<capability>urn:ietf:params:netconf:base:1.1</capability>
</capabilities>
</hello>
]]>]]>
#144
<rpc message-id="1" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
#99
<edit-config xmlns:nc="urn:ietf:params:xml:ns:netconf:base:1.0">
<target>
<running/>
</target>
<config>
#157
<interfaces xmlns="http://tail-f.com/ns/test/notif">
<interface>
<ifIndex>11</ifIndex>
<desc>hello</desc>
</interface>
</interfaces>
#23
</config>
</edit-config>
#6
</rpc>
3-Nov-2017::09:12:47.235 **< sess:29 write:
<rpc-reply message-id="1" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
<ok/>
</rpc-reply>
##
#147
<rpc message-id="0" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">
<close-session/>
</rpc>
3-Nov-2017::09:12:47.238 **< sess:28 write:
<notification xmlns="urn:ietf:params:xml:ns:netconf:notification:1.0">
3-Nov-2017::09:12:47.238 **< sess:29 write:
<eventTime<rpc-reply message-id="0" xmlns="urn:ietf:params:xml:ns:netconf:base:1.0">2017-11-03T09:12:47.238394+01:00</eventTime>
<netconf-session-end xmlns="urn:ietf:params:xml:ns:yang:ietf-netconf-notifications">
<username>admin</username>
<session-id>29</session-id>
<source-host>127.0.0.1</source-host>
<termination-reason>closed</termination-reason>
</netconf-session-end>
</notification>
>
<ok/>
</rpc-reply>