Remember Fox did talk about wanting more cohesiveness amongst their X-Men films...actually I believe it was Singer who stated this when it was first announced that "Days of Future Past" was going to be First Class 2's title. So making "The Wolverine" a "sequel" of sorts makes sense with that regard.
Story wise though and everything else I see no reason to be "worried". If it references "The Last Stand" it's not that much of a big deal. Mangold did say that the script re-write that occurred affected 80 percent of McQuarrie's script. I'm guessing this is what it affected now. As long as the bulk of the original story is intact I'm not worried one bit.