There's third party plugs you can use to do that already.
Convert your assets to base64, encode them with one of the encoder plugs, add the encrypted text files to the project files.
Load by url already converts the decrypted base64 images, and there's even an audio plug to play base64 audio(haven't tried it in a while however).
Theres also an audio stream plug which has pros, and cons.
If it really is a big issue for you then you can continue down the third party path for easier methods.
In other words there are options beyond relying on Scirra.
Edit:
Supposedly C3 was to make it easier to work with the sdk, and roll our own plugs.
Of course no way to know if that's part of the free version.