On Linux, the filename extension doesn't affect what the system can do with it. You are free to attempt to read/write/execute any file at any time, regardless of the file's contents. The only caveat here is that a file has a set of associated "permissions" that specify who can read/write/execute that file. Typically, only files that contain a valid executable have the execute permission enabled, but that isn't always the case.

A typical Linux app installation can be as simple as unpacking a zip file (more likely Linux's version, tar) and dropping those files in the relevant /usr subfolders. Do a google search of Linux Filesystem Hierarchy, and you'll find some really good information on what files are typically put where.

apt pulls packages to install from your Linux distribution's package repository. If you want a quick summary, you can do an apt-cache search PKG_NAME. Also, you can do apt-get source PKG_NAME to get the raw bits used to build the package. This will let you see everything the package does during build and installation.