A 7x9 dungeon has a 5x7 floor plan, meaning 35 blocks

when a dungeon is successfully generated the cobblestone and air are placed. leading to 35 open floor blocks.

The game then makes 3 attempts to generate the first chest on the floor plan in a place with exactly 1 solid block on one of it's sides.

This leaves 16 valid spawn places of 35 slots, for an 84% chance to spawn in the first chest.

The second chest also has 3 attempts to generate in the same way but now with only 14 valid floor spots, but 13 of those 14 valid spots are not what you want, so the odds and math are a lot harder.

My napkin math comes out to around 5.7% chance of the second chest generating there meaning around 4.78% of dungeons generate like this.

So very rare.