The Essence STX does have an onboard voltage regulator and power supply filtering for the analog stage. Sure it isn't as comprehensive as a large dedicated DAC, but most of the hard work is already done by the computer power supply. As for having a noisy power source, a decent PSU will have pretty good output regulation and though it may provide power that isn't as clean as what you get in some standalone DAC designs, the additional onboard regulation should give you a fairly good result.
My point is that the same PSU which drives the STX also has to drive your motherboard, video card, cpu, hard drives, etc - all of which vary in loads over time, which causes noise and voltage instability in the power supply. This instability is generally not enough to affect your major PC components, but it will affect hi-end audio components. This is very different from having a dedicated power supply designed specifically for a standalone DAC/amp/output stage/etc.
This is why transformers can be shielded, and also why high-end gear sometimes keeps the power supply in one box and the actual amp/dac in another. Likewise, any other gear you put the external DAC near will also be shielded in its own box. Say what you will, but I simply don't see an external DAC receiving as much EMI interference as one inside a computer. There is a lot going on in there. That is one of the reasons why on-board audio sounds so bad.
This is incorrect, the RCA jacks are a line out connector. When connect via the RCA jacks you bypass the onboard headphone amplifier, you cannot run the signal through the headphone amplifier and still get an audio output from the RCA jacks.
If you were getting tons of noise using the RCA connectors I would suggest that you were doing something wrong. I have used the Essence STX with more than one headphone amplifier without any problems, and I expect that your issues were more of implementation instead of actual flaws in the product.
Ah, I did misspeak when I said that everything goes through the headphone amplifier stage. However, the RCA jack outputs still go through their own amping stage (you can hear the STX "click" over when you change the output method). You can still adjust the volume of this amping stage via the STX control panel (I'm not talking about the Windows audio mixer here). To be fair, I didn't encounter any noise problems when I hooked up my M3 headphone amp to the RCA outs, but, as I said before, I did when I connected them to my Denon stereo receiver, which drives some small B&W speakers. I know the Denon is not exactly the best quality speaker amp, but the double-amping problem did creep up here.
Don't get me wrong here. The Asus STX is a fine sound card for its price. It acts as a decent DAC and headphone amplifier because that is what is was designed to do. If I needed those capabilities in a computer sound card, I wouldn't look anywhere else. However, when you stray from that setup, such as using it just as a DAC, you may run into problems. It simply cannot compete with higher-priced external DACs and amps, but I don't expect it to at it's price.