How to theme output of node_view_multiple()?
The return from node_view_multiple is supposed to be a dumb collection of node render arrays, it's not meant to be themeable in and of itself (at least not on a generic level, obviously case-by-case you can do it). The function sepecifically doesn't get involved with the theming, as that should be up to the caller to determine. So using #theme or #theme_wrappers on the outer array is the correct thing to do. 

There isn't anything you can do to target other modules' use of node_view_multiple() in this respect, short of:


Patching the module code
Patching node_view_multiple itself so it has a default theme function, which you can then hook into.
Use a broader attack like hook_page_alter() to make specific changes to specific arrays when it makes sense to.