The number of bytes per tile defines how many different tiles you can have on the layer. One byte allows for 256 different tiles to be placed anywhere in the layer. If you need more than that many kinds of tiles on a single layer, you'd need to use 2 bytes per tile, which allows for 65536 different tiles. This should probably be enough for any mapper, but if you do in fact need more than 65536 different tiles on a single layer, SGDK2 has you covered. You're crazy, and there's probably a better way to do things, but it's got you covered, because the final option is 4 bytes per tile, which lets you get up to 4294967296 different tiles per layer.
(When I say different tiles, I mean different kinds of tiles. The size of the layer determines the actual number of tiles present on the map.)