If by "this issue" you mean young, single Thai women having difficulty getting US visas, it definitely didn't start within "the past couple of years" - the same complaint has been made by American boyfriends throughout the 30 years I've been coming here, and I'm sure it wasn't new even then. Thailand's relationship to China has absolutely nothing to do with any of this.
Decisions like this one are based on visa law and have literally nothing to do with politics - and the US certainly isn't "punishing" Thailand in any way at the moment.
1) Many decisions were made that quickly even 20+ years ago, when officers had no information about the applicant until they walked up to the window, and therefore could not possibly make a decision in advance.
2) The description of what happened during the interview was completely from the applicant's perspective. Applicants are under a lot of stress during the interview, and often don't know or notice what the officer is looking at or considering, or realize how long the interview is taking. It's totally believable that the officer didn't look at her documents - in most cases they're irrelevant - but the interviewer always looks through the passport (not that that would make her feel any better).
I'm sorry your girlfriend's application was denied, but what the lawyer told you is factually untrue - decisions are not made in advance of the interview.
Ditto for me with the LTR visa stamp in my passport - the guy took about five minutes to stare repeatedly at the visa and the pages before it, look at a chart on the wall, look at his computer, look back at the passport, pick up and put down a few stamps, and then he finally stamped me in incorrectly (he gave me five years from that date, not from the visa approval date). I didn't bother to point out the error, since I knew I would leave again within a few weeks anyway.
The first part of your statement is accurate - from the US perspective, the emergency passport is just a smaller, shorter validity version of a regular passport. Most countries, including Thailand, are fine with that, but I did see a YouTube video in which a guy was refused a visa to India because they wouldn't put it in an emergency passport.
The second part of your post isn't really accurate, though that's not important to the OP. In almost every case where a US citizen is limited to direct return to the US (e.g., an extradited prisoner, or someone given a repatriation loan), that's done with a limitation endorsement in a regular passport. I've seen travel letters issued for prisoners under escort, but that's rare (since many countries won't accept them for exit or transit).
I did this a number of years ago, so I don't know whether things have changed. I was flying overseas on Thai Airways from Chiang Rai, with a change of plane in Bangkok. I wanted to check my bags through and then leave the airport for a couple of hours in BKK, but they wouldn't allow it. My choices were: check the luggage all the way through, go through immigration at Chiang Rai, and stay in transit in BKK; or, check bags only to Bangkok and have to reclaim and recheck them before passing through immigration there. I chose to check everything through.
For those who aren't aware, you absolutely can go through immigration at your airport of origin and transit directly from domestic to international in Bangkok, IF your flights are all on one reservation, AND you're leaving from a participating airport (Chiang Mai, Chiang Rai, Phuket, Samui, Krabi, Hat Yai, Trat). Best to ask your airline.
This has been required for years at CW. I always fill it out with myself as my own "guarantor", and they accept it without reading. It's an utterly meaningless form.