The bank account can be in the spouse's name if the spouse has the money, otherwise the main DTV holder will supply a sponsorship letter and show their Bank statement
Use the group search tool remote worker and read through successful applications and also the keyword of the consulate you'll be using. There's absolutely no reason to use an agent, you seem on top of your game.
She can board the plane using whatever passport the flight was booked under, but then use Thai passport to go through immigration. She also won't need to do a TDAC entering as a Thai.
what you need to show is how you can work online remotely to manage your business, or as an employee of a company where your work is remote. There is no income requirement for DTV, although they might want to know how you survive financially. You need to read, research, and understand the criteria that the DTV is granted for. The best resource would be Destination Thailand Visa (DTV) group search tool, using relevant keywords.
Seems like you didn't provide the proper documentation or didn't provide requested documentation. Did they request further documents? What exactly did you supply with your application?
when applying for the DTV you apply for an entry scheme as either remote worker, or freelancer, digital Nomad etc. There is also soft power entry scheme which includes Muay Thai training attending, seminars or medical therapy. What was your scheme?