I see the problem of extra travel. Let's hope the Thai Immigration officers understand that the German Government is not willing to use EMS service or locate an Embassy close to your home.
According the website of the German Embassy the new passport can be obtained in Chang Mai, Pattaya, Phuket or Bangkok. Why do you have to travel 800 KM to any of these places?
You apply during the last 30 days of your permitted to stay period.
If you stil use the Non Immigrant O visa it will be between 30 days before and the day in the small stamp Admitted until xx/xx/xx which you got on entry.
I have no personal experience, that is why I showed the website and let it in the group. Now waiting for others who actually applied and can tell you how long they waited.
Time to close Stating rules is indeed not enough. The Visa Exempt Entry and the Tourist Visa are desinged for tourists, people who have a break from their jobs and come to see Thailand for a short period of time. But I understand that longer breaks are possible in modern times and you can be a tourist for many years, but for those people different types of visa are designed and believe it or not, Immigration officers are not stationed to carry suit cases. Look on Youtube for multiple series about Immigration in several countries, they all do the same job. Get the correct visa for your puspose and length of stay and the rules are applied, play games to avoid the correct visa and understand the game can be lost.
After 11 years of working in Thailand you should noticed it cost money to be here and tourists do not work inside Thailand even the ones who are allready several year present. We can only advice by telling and explaining the rules, what ever an officer decide when you hand over your passport is his/her decision.