It's not a FiOS thing, it's an MSG thing, but not because the overflow channels aren't available in HD. It's because MSG won't allow FiOS to show them. MSG tried with all their might to keep FiOS and U-verse from carrying any MSG channels at all. The courts had to step in and force them to do so. Part of the final deal is that only MSG and MSG+ are available in HD.
Excerpt from the MSG Wikipedia page:
Since its launch, MSG Network had blocked Verizon and AT&T from carrying MSG HD on any terms through a controversial guideline imposed by the Federal Communications Commission (known as the "terrestrial exception"), that was implemented to encourage investments in local programming, which stated that television channels that do not transmit via satellite uplink – MSG HD's programming is distributed to cable television providers through a terrestrial infrastructure using only microwave and fiber optic relays – have the authority to decide which pay television providers (cable, satellite or telco) can have access to its programming. Because the network was once owned by Cablevision (and remains under common control by the Dolan family to this day), MSG fought attempts by the telco providers to carry it despite the significant rights fees it could collect from carriage deals with those services. On September 22, 2011, the FCC ordered MSG to negotiate with both Verizon FiOS and AT&T U-verse for carriage on each system. MSG and Cablevision used every appeal available to keep the HD channels from being carried by both distributors; however on December 14, 2011, a three-judge panel of the Second Circuit Court of Appeals denied Cablevision/MSG Holdings' petition for review. Verizon FiOS began carrying MSG HD and MSG+ HD on its New York City area systems the next day, and AT&T U-Verse began carrying the HD feeds on its Connecticut systems later that month.