I've run into the same nightmare now as I adopted my Thai step daughters in the UK and eagerly gave them my surname as my wife had two different passports with UK and Thai surnames in 2013 before the rules changed. We applied for the girls' UK passports last year and were told that we had to adopt the girls in Thailand or provide proof that we couldn't legally do that (the passport office don't consider the difficulty of doing that it seems). We withdrew as we thought it would be solved when the girls' Thai passports expire in May 2019. Sadly I discovered this week that even expired passports will stop you gaining a UK passport if the names don't match.
I wish I could have seen this thread before I adopted in my name. It now seems a hopeless unfixable problem. Some sites suggest my wife could change the birth cert in Thailand without adoption being necessary but after reading this it seems not.
The Thai embassy totally ignored me too but did send an email similar to the one described above which was dismissed by the UKPO.