I've only seen pixel art parallax style maps at a very, very small size, because pixel art gets exponentially more difficult the larger the canvas is. It's backwards from anti-aliased images, where going bigger makes things mostly easier. For the pixel look tiles are easier and faster, and add to the authenticity of the look. Tilesets are just plain lots of work no matter how you do it, there's no getting around that. And sadly, as much work as you think it is, you are probably underestimating it significantly. This is why I always push so hard for new artists trying to do a brand new, replace everything tileset. Starting from scratch as someone completely new to tiles means that you will not get to the point where you can start mapping before burnout sets in. That's really disappointing and can make people think they've failed at creating tiles as a whole. Starting with existing tiles not only gives you a good artistic foundation to copy until you're ready to do your own thing, but it means you'll be able to start mapping with your tiles right away. That, in turn, will hold off the burnout since you're succeeding as you go. No matter where the burnout catches up with you, you'll still have useable things.
One thing that you could do without using upscaled tiles or plugins is to use tiles from other scale sizes to create your own 48x48 tiles. Archeia did something similar to this when putting together the DS and DS+ tiles. They DS engine uses 24x24 tiles, so she used the tiles without upscaling and just heavily edited the ones that had to work on the grid so that they worked at the new size, either by partially tiling them within the tile and reworking the seams or upscaling them and fixing all the numerous resizing errors. The rest of the stuff could just be carefully arranged. Or you could just use the stuff from a different set that doesn't depend on the grid and make anything that needs to repeat from scratch yourself. This means you'd be doing all the A tiles, but it's still less work than from scratch.
Anyway, I know lots of possible art, just need a starting place before throwing tiles at you. Some of the Aveyond tiles are even free to use. I like to start with the sprite base and work from there, but you can do it the other way around too.
If you're doing a lot of maps you shouldn't parallax them all. Creating tilesets is more work at first, but once you've got the set up how you want it, everything gets faster and easier and you can just keep adding them. The work per map gets less the more you make. Parallax maps are the same amount of work for every single map. For a few maps it's faster per map than a tileset but that difference gets used up quickly. If it's the grid bound look you're worried about, check out Yanfly's doodad plugin, which makes for a fantastic middle ground, almost best of both worlds solution.
The Make Seamless tool in GIMP is a tool for anti-aliased images, it'll mess up your pixel art. Not really all that fantastic on a lot of raster art either, honestly. I guess using it depends on how true to the pixel aesthetic you want to be. Krita has a canvas wrap feature that functions more like how Pyxel Edit wraps the tile area, but Krita isn't very good at pixel art. Free though, so potentially worth trying out. Pyxel Edit isn't very expensive though, and there's a free, very buggy, much earlier version you can download (save very, very often if you use it). Even completely buggy and missing some significant parts I still think it's a very useful and worthwhile tool for making pixel tiles.
