Your biometrics (face photo + fingerprints) will all match one person, regardless which passport that person carries. So, immigration will know you hold more than one passport. As to what Thai immigration says about it: I don't know. Good luck.
Yikes, good luck. KL embassy ain't playing. If you can't provide everything you can leave it for over two weeks so that the application is cancelled then apply elsewhere.
Thanks for sharing. Is it easy to sign up for TrueMoney? What are the requirements? Are all nationalities eligible? Lastly, where to find TrueMoney kiosks?