I've never heard ANY visa agent say anything positive about the DTV. Anybody, from any country, can apply for it, anytime, while NOT in Thailand without the need for an agent. That's why they hate it! People who use agents for DTV are just lazy or stupid.
I did receive an email containing the payment receipt. On the application site you can also check the status there: pending this, pending that...you may or may not get emails before the final result.
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.