Is it possible to generate a .hex file with MicroPython and my own python program code at a Linux command line, rather than in one of the editors?
Looking at the tag in your question, it looks like you want to use MicroPython on the BBC micro:bit, correct? If that's the case then youu can use this Python command line tool: https://github.com/ntoll/uflash/
Instructions on how to install it and use it can be found in the README at that link.
This works with Python 2 and 3, and your Linux distribution is very likely to have at least one Python version available out-of-the-box.
If you have pip installed you can easily install it with: pip install uflash
But you can also download the source code, using git or downloading a zip file from GitHub (https://github.com/ntoll/uflash/archive/master.zip), and run it without installing anything. In this case you can execute the uFlash script with Python:
python uflash.py path_to_your_code.py
And the current version of uFlash includes the latest version of MicroPython for the micro:bit.