Good stuff in your post. I guess you could count me as one of these newbs with that kind of set up. (iphone w EQu>LOD >Fiio E11>JH16 when they get here.) Right now I'm using SE530 and it sounds pretty d@mn good IMO, for what that's worth (see my sig).
I think it's important for people like me not to gush about new equipment just because they are excited about it, or think it's the end all be all. I don't expect audio nirvana, but about as close as I can get in a truly portable setup that can make my work grind as pleasant as possible for 40hrs a week without my coworkers asking too many questions about my weird expensive equipment. Also I can go walking without lugging along a separate DAC and Amp strapped to my iphone, and take calls without trying to work around giant rubber bands holding everything together.
One small amp sitting on the desk to clean up and improve the sound a bit while I am sitting at the computer isn't going to stick out too much. However a giant stack of gear held together with rubber bands and weird fancy cables, and a big set of cans is going to attract alot more attention than I want. And probably I will need some big expensive open back cans to match what the JH16 or even SE530 can give me in terms of separation, detail, and over all SQ. (And I don't want my coworkers knowing I listen to Enya or Mr. Mister sometimes, so open back cans are a no-go
) So the IEM customs route was the way to go for me. Also I like to listen while I am going to sleep. So it's not like everyone that has an iphone/IEM setup is doing it without some reasoning behind it. I would not compare it to a desk top set up with a top notch set of cans. I have not experienced that yet, I'm sure it is great, for me it's just not the most effective use of audio money to suit my lifestyle, though I am sure it may be superior in some ways. I just wouldn't be able to get as much use out of it.