Of course they stopped in Dubai, that's why they asked. Or did you just think they circled Dubai a couple of times but didn't land? They put the Dubai-Bangkok flight number into the arrival card
Just be aware that an agent using their money to get the visa/extention of stay basically means you have a fraudulently obtained extention of stay and if the sh*t hits the fan you'll be covered in it!
The Non Imm O is the VISA based on marriage. The 1 year extension of stay isn't a visa at all, it's exactly what it says, an extension of stay based on marriage.