bzt, "Part1, the Physical Layer" is not the whole specification. It doesn't specify everything, other things are specified in other parts of the specification and are mandatory. when you ignore this fact, pointed several times to you by different people, in different style, you look a little bit strange. the part, that specifies the volume structure and file structure is called "SD Memory Card Specifications / Part 2. File System Specification Version 1.0". Version may vary, of course. Look it up on the web, and you'll find out the clear answer. like it or not, but this is how it is.
as of element14 and RPi. element14 reproduces the latter as it has been designed, it's not their design. They also make other open boards, like Beagle Bones. I do own one of such. These BB guys added eMMC on their boards, in addition to the SD slot - a wiser decision, so the OS (whateverOS) can live there with whateverFS it loves and SD card could be used with what it is meant to be used as FS (FAT) as removable storage - a much more suitable use case for the latter. eMMC is most often soldered on the main board, so it's much better to put OS there to not mess things up. Also, they are faster. SD cards as the target storage for the OS installation is not a good idea from the very beginning. SD cards were designed to serve the role of removable storage media. The only reason why there are SD card-only boards like RPi is cutting off on prices. Since linux can't live on FAT, they sacrifice compatibility, because they don't have choice. I told here already, when the topic hadn't degraded into these silly arguments with you, that on bare NAND storage devices, it's totally damaging for the NAND to put there ext4 or any other general purpose block oriented FS. Still, since the guys behind UBI/UBIFS gave up on supporting MLC NANDs, from now on, any new linux coming to such boards will smash that poor NAND mercilessly. But what's even worse, in most cases, all those linuxes have been coming with formatted ext4 without any supporting wear leveling layer beneath, even when UBI/UBIFS didn't discard MLC NANDs. Look at Cubieboards, Olinuxinos etc. they all come with ext4 on bare NAND. What does this prove? That they, whoever produce those images, don't care, nothing more. But per your logic, it's a proof of ext4 suitablity for bare NANDs, isn't it? *sarcasm
RPi also lets overclock SD cards to gain a little increase in the slow throughput - very bad move. Of course, you'd believe, this also wouldn't shorten cards' life span, since it's made by element14, *rolleyes but you know what - it does shorten cards' lifespan. because they aren't supposed to be used this way. They, who designed RPi, would be much better off to add support for UHS-I modes - that would increase throughput up to 3 times, lessen power consumption without exposing cards to any damage. But they haven't added this. Why? UHS-I is not something too new, too expensive. UHS-I cards are cheap and very ubiquitous for a long time. there are newer versions of cards - UHS-II, UHS-III and even freaking SDe - SD Express, using NVMHCI and being able to reach up to ~1GB/s of throughput (versus ~25MB/s of pre UHS-I, with 3.3 V signaling, your "brilliant" RPi could only use). They didn't care to add that. Despite most SD/MMC controller IPs, used in modern SoCs, are capable of UHS-I! So maybe they didn't care about incompliance with the SD specification as well? After all, a beardy community guru always can say - hey, your card was just a counterfeit sh1t, buy another one.
In sum - the specification, telling you that FAT is the part of it is not a proof for you, that FAT is the part of the specification.
element14, that makes RPis the way they were designed is the proof that FAT is not the part of the specification.