I'm pretty confused by the last bubble here. It's obviously referencing boke/tsukkomi, but is the 所 here literal, figurative, or part of a set phrase?

Literal.

In a nutshell, Meiko is commenting that Rin should be worried about Miku wanting to eat (tako)Luka instead of worring about Miku/negi.

Okay, that's more in line with what I thought it might be. Thanks.