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willpowered
Seconded! I registered on the forum today specifically to suggest this. (I mean, I'll probably make more suggestions later too, but today I'm here for this!)

The problem for me is that when OpenGL goes to sample the color on the texture, it mistakenly interpolates the zero alpha padding pixels with the pixels of the tile.
Depending on the position/zoom/rotation of the camera, it can look pretty ugly in-game.

Very nasty seams happening there! Although the tileset looks nice when exported by Pyxel Edit, it's actually unusable in-game.
My current workaround (using libGDX) is to export the tileset from Pyxel Edit as individual tiles, then repack them with the libGDX Texture Packer, with the duplicatePadding flag set to true. This does what TheReverend's example image shows, and makes the tileset usable.
