Yes, turn "export_large_sheets" to "always" - this is responsible for outputting ONLY spritesheets with "type": "single". These are those oversized spritesheets with frame size 192x192 that will export individually when you have weapon on, one sheet for slash, walk, etc....
Open lpc.layout file and in the very first spritesheet with "name": "universal" change the value of "type" from "universal" to "single", just as is shown in my previous screenshot (highlighted part in the notepad on the right). This will export that default big spritesheet, but in oversized format,
Turn all the other animations to "type": "universal".
Now your export should be only one big spritesheet with oversized frames, regardless if you have equipped oversized weapon or none at all, or if you export the full equipped character or only a piece of armor, or only a weapon with hidden body.
However, that default spritesheet does not have "smash", "whip" and "fish" animations. You will have to add them to the "frames" yourself if you want them in that same single sheet. This is where you can change the layout of your spritesheet, if you want to make your own. Just be careful about commas and typos, or the app will crash. Doesn't hurt to backup the whole data folder.
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Bow to you good sir for making this thing. Looking forward for future updates.
If I may, I'd suggest you add option to show body accesories (such as hair, beard, ears, wings, bloody eye, ... ) when "Show Body" option is unchecked.
Addition of grayscale palette or "white color" to each item would be cool. It would open up an option to have items in any color people want via modulation.