Super Mario World is set during a period of Thwomp history where domestication had become commonplace, but armor chiseling was still being tested. You'll notice that other appearances of Thwomps with seemingly unchiseled hides are visibly smoother, and often a different color, whereas the hides of Super Mario World Thwomps are the same color as their main body (torso?), and very rough-looking, likely showing that the practice was being developed, but still hadn't made too much progress yet.

Alternatively, Dinosaur Land, already known to have islands that can respond to stimuli and odd variants of existing creatures such as the Jumpin' Piranha Plants and the Galoombas, has a rougher and less docile variety of wild Thwomps as native creatures, which may have been captured by Bowser out of necessity, inspiring the idea to attempt to domesticate and weaponize the standard Mushroom Kingdom Thwomps. The Dinosaur Land Thwomps have a distinctly light-gray color and a round-er, uneven face with black eyes and white pupils. The Galoombas were later imported back to mainland Mushroom World, but the Thwomps were not, likely due to their unruly and hostile nature being dangerous to their handlers.

Some docile Mushroom Kingdom Thwomps from a safer time clearly have been hidden out somewhere until recently, as they appeared simply sitting on the ground contentedly as obstacles in the Kingdom Builder portion of Super Mario Run.