So, I don’t do clips. My batteries have tabs on them and get soldered to the power board. That’s as firmly as you can get that.
And yes, you essentially just described what I already have designed. Mine is two separate boards that get stacked together; a power module and a controller module. Power module has both the charger on it as well as a 5V/1A boost circuit for the controller. On the controller, it’s a 32U4 paired with an SD card. Since the strips don’t have a CS/SS signal, they’re bitbanged on other pins. There is a master power switch, but there are also two additional tactile buttons which can be programmed to do whatever. One of them is on an interrupt pin, the other isn’t. There are plenty of pins available still, I just didn’t route them to anything because I know I won’t need them … right now. Maybe in the future I would and then I will have a Rev. 2 of the controller.