Wow, now I'll have to go home and look at my Sidi Genius Megas.
Like the OP, I've occasionally had some issues with the top of the tongue, but (a) I could usually solve it by loosening the ratchet and repositioning the tongue; and (b) since it is "leather" (of some type? I think?) once I got going it would soften up/absorb moisture so it was only a problem for a few minutes. I could see this being a problem for others, though (drier climate/not heavy sweaters/different socks/different anatomy/more sensitive skin/etc.).
The snipping does look like it would solve the issue, now I have another reason to look forward to going home after work.