I messaged m7600, the author of that page, to let them know.

In the meantime, there is also this page, which also covers creating a map for Flare. The only difference is that tutorial doesn't use flare-game assets.

Whoops! I seem to have lost those files. I'll try to fix that tutorial, but it won't be in the near future, since I'm swamped with work from my day job right now.

In Tiled, each tileset has a single tile size. For the "base" part of flare-game's tilesets, we use 64x128 tiles. The "wall" tiles use that entire space, but smaller tiles will use the bottom 1/2 or 1/4. For tiles bigger than 64x128, there are two options. Either slice them into 64x128 chunks, or create a separate tileset for the larger size. For example, the dungeon stairs tiles are in their own tileset with a 256x256 tile size.

If you're creating your own tilesets in Tiled, I recommend looking at flare-tiled-tools. This extension adds an export format to Tiled for Flare's tileset definitions.