I'd see it this way: Using Modernizr (and browser tests) to load Javascript files is a very general design decision everyone on your team needs to be aware of in any case.
However, you probably want to implement (if you haven't yet) some sort of initialization of your application, which should be the last thing to be run — after everything has been loaded. This initialization can then be executed in a yepnope callback, apparently even within a $(document).ready()
wrapper.
Yepnope states in this context in the "common gotchas":
Just because your script is done, doesn't mean the document is ready.
Don't forget that you can use document ready callbacks inside of your
yepnope callbacks. If you're toying with the DOM, we'd heavily
encourage you to do so, because your test environment may act
differently than your production server the speeds are dramatically
different.
And for the sake of completeness:
Without checking them any further, here a couple of other ideas on how to deal with document.ready + Modernizr.load
: How can I use yepnope.js with $(document).ready() effectively? and https://stackoverflow.com/a/6767886/564721