I've just found that mw.makeProtectedEnvFuncs can be accessed from modules with the code require( 'mwInit' ).makeProtectedEnvFuncs. This doesn't allow overriding the allowEnvFuncs setting,[1] but given that mw.makeProtectedEnvFuncs was hidden from modules with rELUA1efe182e it seems like unexpected behaviour.
[1] Example of trying to use getfenv:
setfenv, getfenv = require( 'mwInit' ).makeProtectedEnvFuncs( {}, {} ) getfenv( function () end ) -- Error: attempt to call upvalue 'old_getfenv' (a nil value)