I actually do use a base custom palette in my hacks. I made up this patch a while back, and it's worked fine for me:
rep 512 : dl $07E565
base_palette.bin is basically just a renamed .mw3 file, and $00B2C8 and $00B2F0 are for player 1's normal and fire palettes. (Replace them with the color values you're using, and add $00B2DC and $00B304 if the hack has a 2-player mode.) You want to apply this ONLY ONCE, after saving a level with a custom palette in Lunar Magic (and applying the Super Scratch ROM patch, preferably, otherwise levels with data in the $07E565 area will glitch up...or you could just change that address to some other freespace location) but before actually making any levels.
But yeah, I agree; it could be handy to have such a feature built into Lunar Magic. I'd even like to see a palette index kind of thing where you don't need to overwrite the entire
base palette but have separate pointers to the palettes for sprites and the three background layers. I'm probably about the only one who keeps my palettes organized enough to benefit from that, though.
I'm working on a hack! Check it out here