I get what you're saying, but when I read those I would never have considered your interpretation. I probably would have written the rule the same way they did because the posited ambiguity would not have occurred to me.
For starters, both the card and the rulebook refer to precisely two territories. It would be a stretch for me to read that as "for each lake, pick two territories that border it; the chosen territories are considered adjacent this scoring round." And, of course, if they had meant "all territories bordering lakes are adjacent" they would have just written that. Lastly, I'm pretty sure the either of the latter interpretations would be extremely powerful compared to other cards.
Obviously, I have no inside knowledge, and people write some pretty dumb things in rulebooks sometimes, but until someone official replies, I think all of the natural indicators would suggest this applies to exactly one lake.