TexturePackerImporter addon actually works with both Texture Packers (Free, Paid).
1. .tres files stores at different folder this is double work, grab from one and place to another.
2. tilesets don't support multiple .tres files, so you must do tilemaps for each 1 tileset. That is huge problem -> https://github.com/godotengine/godot/issues/35756
3. there is no auto-renaming, if you rename coin.png to coin1.png you will get coin.tres and coin1.tres
4. there is no auto-deleting if you did 3point, go to different folder and delete for yourself.
5. re-importing generated files takes long time even with little changes, renaming, deleting, adding 1 sprite.
that is all for now.
Waiting for Godot 4 now, native atlas-texture will be re-written not soon.