Yes, I will be either using that wrapper or my own

You can ignore those warnings, I'm seeing them as well.
after last update i have this error
user@netbook:/home/user/gekko# node gekko config=config/user/cexio.js
/home/user/gekko/config/user/cexio.js:1
(function (exports, require, module, __filename, __dirname) { \// Everything
^
SyntaxError: Unexpected token ILLEGAL
at Module._compile (module.js:439:25)
at Object.Module._extensions..js (module.js:474:10)
at Module.load (module.js:356:32)
at Function.Module._load (module.js:312:12)
at Module.require (module.js:364:17)
at require (module.js:380:17)
at Object.util.getConfig (/home/user/gekko/core/util.js:18:15)
at Object. (/home/user/gekko/core/util.js:144:19)
at Module._compile (module.js:456:26)
at Object.Module._extensions..js (module.js:474:10)
add: problem solved !
just delete first slash in setting file.
Well those config files are extremely outdated, please use the file `config.js` and read here how to configure it:
https://github.com/askmike/gekko/blob/master/docs/Configuring_gekko.md