We have a distributed monolith that's 20-30 years old, that has various systems written in various different languages interacting with multiple interconnected databases. We're working on migrating all of it to python, using django models.

The key thing in a system like this, that was kind of stumbled upon by previous devs who started the python migrations, is the database should be treated as its own independent unit and managed separately from the individual applications that connect to it. For example, we've defined the django models in an independent library that the individual applications import. It also contains the configuration for routing queries to the different databases - only takes a couple of lines of boilerplate in the application's settings file.

We haven't yet switched to using django migrations and are still doing updates manually, but after some work the past couple of years it would now be an option. They would go in the common library, avoiding the pain points you've listed, and could be run from any application that needed it - django tracks the migrations that were run inside the database so they'd all see the same thing and act the same way.

For us, it has absolutely been a major benefit.