Also, this is constantly repaired, updated, etc., not just thrown away and replaced by another one.
http://www.collectspace.com/ubb/Forum14/HTML/000534.html
There's at least 20K HSRI "model numbers" and over the years probably many more as revisions were made, they made lots of Q+A test pieces and there were many revisions and lots of repairs and there's a lot more than just black HRSI tiles, I'd estimate somewhere in the realm of "way more than 10M tiles" were made over the years. The hotter they get the smaller and thicker they have to be, something about differential thermal expansion stresses or something.
The TPS as a whole was quite a technological accomplishment.
I believe this pix was taken in the post-FIB era. Flexible insulation blanket. Not all tiles could be replaced by FIB but some could and were. I imagine the heat load was not very high in those positions, so FIB makes sense. And I know FIB looks exactly like the wavy blanket quilt look you're talking about and is seen in the pix. FIB had another name which I forget. The nomex based "frizzie" (FRSI?) looked less quilt-y, more like a prom dress fabric, well, kinda. I don't see anything I recognize as frizzie in the linked pix. Frizzie looks like the inside layer of a firemans coat, which also probably doesn't help describe it very much, yet, there it is.
TLDR is that wavy tile is not a tile, its a quilt.
Most people know the engines were under continuous development for practically the whole program; well, so was the heat shield system. I can't be bothered to look it up and it doesn't matter anyway, but I don't think the same TPS configuration ever flew more than three or so times in a row without some new idea being tried, at least in the early decades. Continuous integration.
Personally I always suspected we'd lose more orbiters due to continuous integration fiascos than mechanical damage. Then again they spent a lot of money on research, Q+A, and experimentation so what would be a disaster in a typical IT shop works pretty well in aerospace.
Smaller tiles are easier and cheaper to replace, and thus the uneven look.