Because the world is just full of airliners with ejection seats.

It's a technology demonstrator. They are testing a technology. For the reading challenged:

The X-65 will be built with two sets of control actuators – traditional flaps and rudders as well as AFC effectors embedded across all the lifting surfaces. This will both minimize risk and maximize the program’s insight into control effectiveness. The plane’s performance with traditional control surfaces will serve as a baseline; successive tests will selectively lock down moving surfaces, using AFC effectors instead.

This isn't new. Any large aircraft is going to have hydraulically driven control surfaces. Where do you think the hydraulic power comes from?

Large aircraft have APUs and/or battery backups so that they can still be controlled if the engine(s) die.

> So if the engine shuts down you lose control of the plane?

Maybe. It may eventually have a RAM air turbine (https://en.wikipedia.org/wiki/Ram_air_turbine) to generate electricity (possibly also to directly get compressed air)

They may also only use such a device to compress air, and power the controls with a relatively small emergency battery.

I think none of those will be ideal, but modern fighters already are unstable in flight, so this doesn’t look like completely new territory to me.

It's DARPA, its probably intended for a drone.

Airliners, even if they lose the big engines under the wings, still have a small one in the back, called an APU, that can provide power and bleed air (!) for all kinds of critical systems. A hypothetical airliner from the future relying on active flow control would absolutely have several redundant systems to ensure controllability.

Most planes have at least 2 engines. With careful design you could make either produce sufficient air for full control.