As I said earlier, you can go over 40mm for the stack height. It's in the rules!
The rules say 40mm is the limit for a size 42 (US men's 9) and that they can increase "marginally" as the shoe scales to larger sizes. In another article today discussing the new shoes, a Nike VP is quoted as saying the Alphafly is 39.5mm (for size 9) but that since Kipchoge wears a size 10.5, his legal shoes are 45mm.
And this is not the start of pros having to live with inferior shoes or equipment. You think Skechers makes trainers or spikes that are better then everyone else's? Only a single company can make the best shoe for an event. Everyone not wearing that shoe is at a disadvantage. Same with the bobsleds in the winter olympics or guys wearing some crazy brand of shoes you never heard of in the NBA because they backed up the money truck.
You don't have to wear to the same shoes as everyone else for it to be fair and a level playing field. And WA has made sure that athletes have the opportunity to wear the best shoes available.
No longer will the Olympics be the ultimate battleground of new technology in custom prototypes for a handful of selected athletes. That's a great thing for the athletes and runners everywhere. Sucks for the shoe companies who now can't test any prototypes in competition and have to make their shoes available to anyone who wants to buy them.
No one is forcing anyone to wear inferior shoes - except for the inferior shoe company contracts. But hey, they are paying you to wear their inferior products. If you want to have the best, then get an apparel only deal or other sponsor or get your contract reworked. One of the worst things about track & field is that the shoe companies are almost the only athlete sponsors. Be like LoLo Jones or the Ingebrigtsen's and get sponsored by Red Bull. Hell, get RunGum to sponsor you. Get endorsement deals from sunglasses, autos, underwear, and water and health care companies. LeBron endorses over 12 different businesses. This is what it means to be a professional athlete. And if you don't like your sponsors products, maybe you shouldn't be hawking for them.