This also serves as a guide so the NSA knows what to target
If they see an ISIS training manual saying "use this app available from this third party app store" they're going to hack that third party app store and plant a backdoored version of the app there that p0wns the phone and sends traffic to them. There is probably nothing connected to the internet that could survive a directed attack by the NSA, since they probably have a whole library of 0 days for every conceivable server or device at their disposal, along with other techniques like social engineering or even black bag operations if necessary and the target is high value enough.
Honestly even if Android and iOS were known for absolute certainty to be backdoored they'd be better off communicating with those using standard tools like iMessage, as they'd be much better off hiding in a sea of billions than using some app off a third party app store that maybe has a few tens of thousand users worldwide and acts as a lighthouse alerting the NSA "I'm likely to be a terrorist" through its use. The NSA probably reads that guide and hopes the terrorists follow it to the letter.