Basically, it's meant to encourage you to take a "Main" ability as your Supernal, rather than a "support" ability, rather than outright forcing you to do so.
Which is good design space, actually.

Now War is actually a pretty great example of a support ability. You pretty much only use it when you have an army around. In the vast majority of campaigns, that'll not be all the time. Even if you do have an army around, you'll still want to have other abilities (combat abilities or performance etc.).

Ride is another ability which has no Essence 4 or 5 charms. So does Thrown actually.
Awareness has no Essence 5 charms.
Dodge only has one Essence 5 charm, and no Essence 4 charm. So does Resistance.
Linguistics has no Essence 5 charms, and only two Essence 4 charms.

Of course, you can build characters who focus on one of those - a legendary Rider, or of course someone who exclusively uses Thrown weapons.
And it's good that the game doesn't prevent you from doing so. But it is equally good that it makes you consider it, by making you think "wait a minute, do I really want this as my Supernal? It has no high-essence charms."


Of course, by taking ANY ability as a Supernal - even if it has no or few Essence 4 or 5 charms - you'll essentially be better in that area than anyone else after character creation, and for quite a while to come.
Sure, once your group is at Essence 3, you might regret that choice. Now your circlemates could become just a good as you in your own area of specialty. And you can't be as good as them in theirs.
But then again, getting Essence 3 charms in their area of specialty will make your pretty damn good at it. So while it's an issue, it's not an overwhelming one. And considering how long it takes a normal game to get to Essence 3, the early boost is well worth it.