I have been testing this with 16x16px tiles, and yeah, the tileset shrinks! So you can just take the same images, downscale them to one third of their size so pixels are 1x1, and it will work the same. The number of available tiles will be the same no matter the tile size. Same thing with character sheets, you can just take a regular character sheet and downscale it to one third of its size and it will work fine with the 16x16 grid.
For compatibility purposes, I'd recommend keeping the triple size version in your asset packs (since most people will stick to the default 48x48px tile sizes) and also add a 16x16 version for the people who'll use a native 16x16px grid.
Hope this helps. Thanks for your work! <3