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.