This being my first post here, I must state, in advance, that I think phalcon is one of the easiest, fasted and cleanest frameworks I've had the pleasure to use. Now that that is out of the way...
So we have an immutable architecture... Our application servers are constantly being built up from base images. We never maintain state on our servers. Phalcon migrations, unlike almost any other migration keep the migration state in the database. By using a file in the source code directory this creates problems for us that we need to solve with jank and gorilla glue. Luckily we specialize in jank and gorilla glue. If you have an opportunity to introduce a migrations table and maintain the state there I would love you even more.
Best Wishes