Already more than 2 months overstay, you are aware that with a few more days you will hit the 90 days and that will save your worries to get back into Thailand for at least 1 year.
The emergency travel document and back to UK was the best option.
There might be a small issue. The under consideration period is used to consider if your meet all the requirements, one of them is if your marriage is de jure and de facto.
This is done by a visit to your address and can not be done if you spent the time in Korea.
So the worst thing in life is going to happen, you have to discuss with the officer if you can leave and can use a re-entry permit in this period.
Your old passport is invalid to use, you need to use your new passport and fill in the number on the notification form. You need to transfer the stamps before you can register your 90 days of stay.
You signed but you did not follow up what you signed. It could bite you in the a.. when you try to do this again, this counts for Immigration as well as Ministry of Labor.
Be aware what you sign, telling I did not know does not count when your signature is under this text.
What happened is that the officer you handed over the documents is very capable to check if everything is in order but does not have the authority to stamp your passport. All documents are now at a supervisor to consider, it is rear that during that period an application gets denied,.
You go back on 31 October and normally get the visa and a new 90 day stay or in worst case scenario a stamp application not approved and 7 days to leave the country.