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Nice progress — the grass/sand read is already clearer without the grid.

On the water transition: the harsh line usually comes from treating shore like a third “terrain” painted by hand. Two things that helped me on similar top-down sets:

1) Split the problem: a soft **shore/corridor band** (sand→shallow water) separate from the deep fill tile — fewer pixels fighting on one tile.

2) Keep the grass outline lighter (you already spotted that) *and* let the shore tile carry a bit of grass fringe so the Y-flip grass doesn’t feel mirrored against sand.

If you want to iterate on shore/path overlays without repainting every edge variant by hand, I built Tile Surgeon for parametric border + corridor tiles (square/iso/hex) → export PNG for Godot/Tiled: https://sprite-surgeon.itch.io/tile-surgeon

Happy to sketch on a screenshot if you drop one — water edge is fixable without covering it with animation alone.

You’re not alone — depth bands + shoreline edges are where tilesets get noisy fast.
Palette tip from the thread is solid (desaturate/darken deeper bands). For the edge between land and water, a dedicated transition/corridor set usually reads cleaner than forcing one noisy texture to do everything.
If you want to generate shore/river-style overlays from materials instead of hand-painting every edge variant: Tile Surgeon (Windows) does corridor + border blends for square/iso/hex — https://sprite-surgeon.itch.io/tile-surgeon · demo https://www.youtube.com/watch?v=LqhijXW_MXE
For pure pixel look, animating a few water frames still helps a lot (as others said).

Corner-type terrains are unforgiving: if even one edge/inner-corner variant is missing or mis-assigned, fill tools leave holes.
Quick checklist: confirm you have a full set of outer corners, inner corners, edges, and the solid fill — then assign corners consistently for each terrain.
If the missing piece is actually making those transition tiles (not just wiring them in Tiled): I built Tile Surgeon to generate border/corridor variants from materials (square/iso/hex) and export PNG ready for Tiled/Godot. Short demo:

 — https://sprite-surgeon.itch.io/tile-surgeon
Happy to look at a screenshot of your atlas layout if you share one.

This is exactly the kind of manual tedium that pushed me to build a tool for it — Tile Surgeon generates the border/transition tiles automatically for square, iso, and hex grids, including a corridor mode specifically for roads/rivers cutting through terrain. Doesn't solve the RPGMaker-format question directly, but if anyone's stuck hand-painting Wang-style transitions, happy to share how it handles it: try Tile Surgeon