When working with really small things, the copy/paste grid is really annoying for several reasons. Obviously having to use the arrow keys to move less than 4 pixels at a time is a problem, as well as accidentally shifting parts of the paste outside the rectangle. Plus the border of the paste area gets in the way, since particles can be right next to the edge.
I think that it would be better to just get rid of the grid system (for copy/paste/stamps) entirely, as well as moving the paste area border out 1 pixel so it doesn't cover up part of the stamp.
And as for the problem of copying walls, well there are a number of possible solutions.
You could just make walls align to the grid when moving the paste around, though this might look strange.
Or lock it to a 4x4 grid when there are walls being pasted.
I'm sure this system made sense when walls were a major part of the game, but now hardly anyone uses them anymore and it doesn't make sense to limit the copy/paste system just based on one mostly obsolete feature.
It's not so much that the arrow keys are hard to use, but just that they're really slow. As for making patterns, yeah it's nice... as long as the size is a multiple of 4. (Maybe it would be better to allow snapping to ANY grid size somehow, though I'm not sure if there would be a good way to control that)
Oh and I completely forgot about ambient heat/pressure. I'm not sure that copying pressure was an entirely good idea to begin with, but either way "option 1" for walls seems like it would work fine, where it just aligns walls and pressure cells to a 4x4 grid and lets other things move freely. Perhaps there could also be a key which locks the stamp to the grid to make working with walls (and patterns) easier.
That sometimes cannot be done when trying to copy something out from inside something else.
copy it then paste it then add the border?