Miro,
What apps are you looking to install ? Some apps can be tweaked to run natively using “qnapware” packages. However I’ve not found a way to get these to start automatically on boot so need to SSH in and run a script every time the NAS is rebooted. Alternatively, you might be better off creating a Ubuntu or Debian based docker container and installing your apps within the container to do what you need. I have started to look at this for a VPN app called “softether” and it works quite well.
Cheers,
JediNite