I'm not sure I'm making the connection between YES and the NBC-HD East signal but here goes...the national NBC-HD signal is NOT on a spot beam (it's national).
If you subscribe to MLB EI, you will get all live games (that's the whole point of EI, to allow fans of say, the Yankees, to watch Yankee games in say, Kansas). The only exception to that rule is the games that are transmitted locally over the air on New York Channel 9 (WWOR) which are usually Friday night games. Since WWOR has an exclusive contract with the Yankees for those games, they are not available on MLB EI.
If you were to "move" to a NY address, the YES network would be part of your regional sports package and then you would get the games that way, BUT once again since New York channel 9 (WWOR) is on a D* spot beam, you still would not be able to see the games that are transmitted on that channel.
As for the HD feeds, D* has been inconsistent with the way they handle the HD games. At the beginning of last year's season, the HD feed was only available to subscribers who lived in the NY DMA, then mid-season they decided to open them up to everyone who had the MLB EI package, but when the football season started, they stopped the HD feeds of the games (even though they showed up in the guide) because they needed the bandwidth for footbal (although they would never admit to it). So with HD its hit-or-miss.
Did this clear it up for you, or did I just confuse you even more?