Obviously, you could never have a "true" national HS championship like you can at the NCAA level, simply because college and university programs basically accept a calendar that is geared toward the championship and high schools don't. You would never, ever have a world where all 50 states would follow anything like that. State associations get nothing out of trying to coordinate like that with each other. Therefore, you will always have states like Florida starting and ending their seasons very early and the colder weather states starting and ending 4-6 weeks later.
But when NSAF and other bodies started trying to have "national championships," one idea was to at least wait until the weekend after the final state meet in the country. That way, everyone at least has chance. Now, do Florida kids want to train 5 or 6 more weeks after their state meet? Very few do. It's much more ideal for those with state meets at the end of May or beginning of June.
As far as Nike and NB having meets the same weekend, there's a LOT of backstory regarding the history of competing national meets, but one thing that holds true is that the later you wait into June to have a nationals, the less likely you'll get good participation for all the obvious reasons. But if you go earlier, you leave out states, like New York and others.
Oh yeah, and Nike and New Balance people HATE each other and want to beat each other head to head, so there's that.
The bottom line is that it is what it is, and will always be imperfect. But these meets are still fun and worthwhile for many, as long as you take them for what they are and accept the limitations.
p.s. Now XC is somewhat better, because seasons start and end closer together and you're not facing the end of the school year and graduation. Nike is pretty close to a national championship and it's nice that it's not the same weekend as Foot Locker. Obviously, there's entanglement with the qualifying meets and it would be great if they somehow merged. Unlikely to happen, though. Foot Locker has a LONG tradition and Nike has become pretty entrenched as well.