lua: eliminate package.loaded write in box modules

There are several reasons to do so:

1. Direct `package.loaded` assignments contradicts with future
   implementation of built-in module overriding.
2. It is common for external Lua modules, so a Lua developer used to
   follow this convention.
3. src/lua/*.lua files already return module tables instead of setting
   them to `package.loaded` directly.

This change follows the idea of the previous commit, see it for details.

Part of #7774

NO_TEST=no user visible changes
NO_CHANGELOG=see NO_TEST
NO_DOC=see NO_TEST