If you use ProFrager's FAProtect to generate custom FreeArc binaries so others cannot open them, all you'd need to do is swap the unarc.dll from the ASIS package with your custom generated unarc.dll to decompress the archives.
This does not encrypt the archives per-se, because if you open them with a hex editor you will still be able to see magic numbers of compressors that you used when making the archive, so you will be easily be able to tell at LEAST the final compressor used if not more. That is, unless, you add encryption to the archive in FA cmdline which I have no idea about. It'll probably just slow unpacking down. If all you want to do is stop people from easily looking at what your methods are, just use FAProtect. Then only skilled people will know
