I’m generally enjoying very good results from Linear 1-Pass autofocus on various scopes (Newtonian, Maksutov-Cassegrain, and Refractors) using the ZWO EAF. I also have a joystick, set up to use a couple of buttons for focus-in and focus-out steps. The Indi Control Panel step setting is always set to zero when I start Ekos, so the buttons do nothing until I change the step setting from zero. It would be great if this new value should be stored for the next session.
I don't have a joystick so can't try this but have you tried setting the Indi params how you want them and then saving the configuration (Options->Save). These should then be loaded on startup.
Might be worth raising the issue on the Indi git site. From what you describe it sounds like the button settings aren't being saved as part of the config (but that's a guess on my part).