First, the main thing to keep in mind is that Tiled's goal is to let you assemble your map tiles into a bigger map. So things outside of this (generating metatiles, palettes etc) are a bit beyond the scope of the core of what Tiled is good for. That said, there are still useful ways of handling these things.
In a couple of my projects, what I've done is create my metatiles outside of Tiled. I've built a really janky tool for doing so, but it lets me define 4x4 metatiles, and associate palette and collision data for each metatile. So for these games, each metatile has palette/attribute information baked in. You can't apply different palettes to the same metatile. My janky tool then spits out a new image of my new "meta-tileset" -- an image that's only used in Tiled for helping me draw maps.
I then draw the maps in Tiled. My build script then reads the Tiled files and turns the map data into data for my rom. So it's stored in rom by metatile ids that Tiled uses. The build script also processes my metatile defintions, so they're available in the rom data. At rendering, it reads a metatile id, then looks up the actual tile definitions for it. Palettes/Attributes are easy, because I'm using 4x4 metatiles, so I just look up the attribute byte in my metatile definition. For collision checks, I read the metatile id, then look up the collision data for it.
If you want to read more about this, I explain it a little more at https://anguna-dev.blogspot.com/2019/10 ... eline.html
That all said, since I started this, Tiled has now added some simple support for metatiles in the application itself. I haven't used them, so take this with a grain of salt, but you can create a metatile set by creating a new map, and just drawing tiles into it in groups, arranged into your logical metatiles. Then, when you start creating your "real" map, you can load that first map as the tileset (instead of loading an image as a tileset). When loading it, you can specify the tile size, and then you can draw with those metatiles. In this case, the big question becomes "how do you handle palettes"? I'm not sure the answer to this question here.