Prototypes are absolutely not banned. Neither are custom shoes. That's obvious from both the plain language of the rule, its context, and the contemporary interpretive history.
Language: The rule says that the "type" of shoe must be reasonably available to all. Not necessarily the exact shoe. What constitutes a "type" is an open question, and it's likely that the IAAF intends to keep it that way. They are providing themselves room to issue interpretive guidance later.
Context: Prototypes and custom shoes have been the norm in elite running for literally the entire history of running. At one point you couldn't get track shoes that were NOT custom. Bannister's first 4-minute mile was run in a pair of extremely light custom spikes. Every major marathon has a significant portion of the elite field wearing custom and prototype shoes. Sometimes it's something pretty new; sometimes it's as simple as marrying the midsole and upper of two different mass-produced shoes. Given the fact that prototypes and custom shoes are routinely used by pros, it is implausible that the IAAF intended to totally revolutionize shoe practices with a vaguely worded rule and no interpretive guidance. It would be different if the rule were on the books and then only after it was enacted did athletes start wearing prototypes. But given that the athletes were doing it already, if IAAF intended to ban the practice, they would have just written, "shoes worn in competition must be available to the general public through normal retail channels," or something like that.
Contemporary Interpretation: The way that people who wrote a rule interpret it is probative of its meaning. After the rule came out, all the elites continued to race in prototypes, and the IAAF did absolutely nothing, which indicates that they don't think it violates the rule that they just wrote.