A guideline is just that..... not a rule, or law that is enforceable or prosecutable.
what you're missing is that the FAA is adding all of this to the current environment outside of the formal rules making process. that application (which I haven't seen yet because I'm traveling) might have that acknowledgement and it may or may not ever mean anything legally because the FAA doesn't make rules that way. Look at it though the way it's intended, they're trying to educate with this new registration process (as well as get records of who is doing what) so if they present a guideline during the registration process and if people see it there for the first time and think to actually follow it, then the FAA has accomplished something even if it's marginally or not at all enforceable.
argue the rules all you want, the FAA has successfully changed the definition of an "AIRCRAFT" to include all models, kites, etc. There are numerous FAR's (Federal Aviation Regulations) that can and will be applied if/when the FAA observes you being foolish so the 400' is a reasonable guideline which, if broken and observed or if broken and which causes an incident, will get you under the FAA's microscope and you'll be lucky if that's all they violate you for.
The moral is, for everyone, don't be stupid and pray you never get into it with a manned aircraft at any altitude.