Since Aseprite does not support layer masks, transparency needs to be manually applied. Creating a manually “rasterized” layer for exporting preserves the original tiles for future editing.

To apply the masks for the sand and dirt pattern layers:

• Select Frame 1 (“Edit”)
• Make edits to “Pattern” Tilemap layer (in Pattern Group)
• Duplicate “Pattern” layer
• Right-click on “Pattern Copy” and “Convert to… Layer”
• Open “Mask” layer and select transparency
• Open “Pattern Copy” and press delete
• Move “Pattern Copy” cel to Frame 2 (“Export”)