Funny how you find the answer just after posting a question. Posting here, in case someone comes looking for it.
As per @Kero's comment above, that's correct. The command-line option will only recognise strings.
There is however an eval-file command that can be used to achieve this (and now that I have discovered it, a lot more).
Here are the steps for achieving the goal I posted in my question, however as the eval-file WP CLI command can be used to execute a PHP file, we can code anything that we deem fit.
Step 1: Create a PHP file with the required code. In my example here, I added the following:
set_theme_mod('my_array_mod', array(1, 2, 3));
The above code will use the WordPress set_theme_mod function to create/update mods named my_boolean_mod and my_array_mod.
Step 2: Execute the above file using the WP CLI eval-file command
wp eval-file my_file.php
That's it. Hope this is useful!