Thanks for getting in touch! I’m sorry you’re hitting some unexpected results during your deployment. The package will still be deployed and extracted to the Tentacle/Applications folder, and using the custom installation directory feature will copy all extracted files to the defined directory. So they should exist in both.
If you’re unable to see the files in the custom directory, could it be due to defining a variable in the CID field, where the variable isn’t scoped to where you’re deploying? I’ll also be happy to look through your verbose deployment logs with debugging variables enabled to get a better look at what could be happening. You can refer to the following doc page on how to produce and export this log.
I hope this helps for the time being! I look forward to hearing back and getting to the bottom of this one.