If docker is chosen to run your backend infrastructure, then you’re probably going to want to abandon the FreePBX managed module updates in favor of just managing them with docker. Docker is basically immutable infrastructure, and the module system of FreePBX doesn’t fit in with this philosophy.
As far as being the wrong tool, for the current state of FreePBX, I will not disagree. That being said, changes can be made to FreePBX to increase support for docker. I don’t know if this will always be the case in the future, but FreePBX needs to be modified to support it.