Leaving Hombu to become independent is not new folks, in fact due to the one representative per country rule many had to. A bunch of top-level sensei left to be independent shortly after O-sensei died. Why did they leave? Ultimately, most likely because they did not choose to "honor" the current hombu authority figures that would judge their Aikido and tell them what to do. Were there other factors involved such as personality types, restrictions imposed from many different levels (organizational, federations, governmental) -- sure probably.
Is H.Saito leaving for those reasons as well? Who knows? He hasn't shared that with us so it's none of our business.
Some of those independents have now rejoined Hombu-dojo, so who knows…maybe H.Saito will rejoin again later in life.
Will it change anything? Only where you get that little piece of paper!
If you train under H.Saito you'll get a paper that says, "such and such rank -- Iwama-Ryu". If you train with one of the other "Iwama-Aikikai converts" you'll get a paper that says, "such and such rank -- Aikikai".
Can you still run back and forth from Hombu to Iwama…I'm sure you can.
Will H.Saito welcome Aikidoka of all styles to Iwama to train -- you bet he will (his father did too).
So who cares!?! End of the day pick the teachers you like, learn all you can from them and seek out any teacher of any style that interests you. In fact grasp at every opportunity to study with great teachers regardless of your (or their) style.
M.Saito's efforts near the end of his life were to get people to see beyond the style barriers and absorb what is good (a fundamental change from his earlier days of criticizing Tokyo). If there is one thing you can learn from him is that the really great sensei (the real masters) are either dead or getting on in years folks -- make the best of their time.
P.S. Iwama is complex. Now there are three levels of separation at Iwama. There were the old students of Ueshiba that trained with him at Iwama who never accepted the "youngster" M.Saito as Iwama's dojo-cho (most are gone but their students are still around), there was M.Saito's students who didn't used to accept Hombu dojo-chos but since H.Saito was named succesor switched teams, and then there are Saito students who accept H.Saito as the Iwama dojo-cho. Old and new conflict entwined…maybe some day they will untangle it, maybe not