Hi! I’m a fairly new Aseprite user. I was frustrated by some of the limitations when exporting spritesheets, so I created an extension to make my life a little nicer. Instead of relying on layer visibility for exporting the sheet, it lets you configure layers (or entire groups) to be automatically ignored on export. It also gives you the ability to mark groups to be Merged on export, which will ensure all the layers in that group get exported as a single sprite. If you like to work in multiple layers for each sprite in the sheet, this eliminates the need to flatten them manually before each export.
I hope other people find this extension as useful as I do!