Unless I'm mistaken, and it's been awhile:
Crono is left-handed.
Miguel is right-handed.
Even if Crono went incognito to El Nido, there's no reason for him to change his dominant hand, especially since he never pulled the "There's something I haven't told you: I'm not right-handed, either!" gambit during his battle against Serge.
Besides, the people of El Nido are sometimes quite xenophobic. If Miguel and Leena were foreigners, somebody would've said so.