Last week, Josh pointed out an oddity in the list of spies in Parshat Shelach, namely, that Ephraim's spy is mentioned first, but only Menashe's spy is considered 'le-mateh Yosef'.
I'm not sure I have an answer, but there's something in this week's Parsha (Pinchas, le-chol ha-de'ot) that leapt out as being relevant to the discussion. The Torah recounts the ancestry of Tzelophchad's daughters back to Yosef, through Menashe. Midrashim point out that there's a common theme of desire to be a part of the Land of Israel. Yosef insists that his bones be brought back, and the daughters of Tzelophchad argues sucessfully to inherit their father's portion.
There's also a theme in the story of Tzelophchad's daughters that considers them to be the tikkun for the sin of the spies (this is from memory; I don't have chapters and verses to cite). Thus, being meyacheis the Tribe of Menashe's spy to Yosef highlights the fact that this spy was indeed an heir of Yosef, but who nevertheless went against the grain of his heritage when he gave a false report. It was the daughters of Tzelophchad who re-asserted the Josephite relationship with the land.