Are you an American? The U.S. has no system of registration like pretty much all EU countries do, and it's fairly easy for a U.S. citizen to pretend to be a resident with a driver's license or other document while actually not living there. Not so for EU citizens.
It would be much easier for you to go to one of the countries close to Thailand, which allow non-residents to apply, like Vietnam, Indonesia, or Taiwan. But you mentioned three children? Doesn't seem like the easiest thing to arrange accommodations for everyone while you wait for your visa decision. Where is your residence now? Can you apply there, before going to Thailand?
Would there be a problem with registering in Germany and then de-registering in a couple months? Because registering comes with a few requirements, like gettig health insurance, which I don't know if you care to do. Because I don't think you want to be registered for a long period if you don't live there--they'll bother you about filing your taxes. And correct me if I'm wrong, de-registering in Germany won't be so simple. You'll have to provide proof of your new foreign address, but I'm sure that you know this because you de-registered previously.
Did your originally submitted employment contract specify authorization for remote work? Thanks for your input--haven't seen too many accounts of applications of Taipei lately. Wonder if word got out it's a tough embassy.
If we're assuming this is true, does not having any money remitted into Thailand (because you don't have a Thai bank account) absolve you of doing a tax return? Maybe it's like the U.S. Even if you don't owe any tax, they want you to submit a tax return anyway.
I think some consulates will arbitrarily add the remote work in Thailand arbitrarily, but it may be possible to get an approval with just authorization to work remotely in general.
In the OP's case, the embassy might have been able to see that the applicant did not know their uploads were being overwritten when they just received the 52nd page of his passport. What's so hard about explaining in one sentence that all pages must be in a single document? Or maybe it wasn't obvious and they really thought OP was just uploading single page documents for the hell of it. Or maybe they don't have the English skills to say that. Anyway, the embassy should have the courstesy to be more clear with the application fee being paid.
I have a sticker visa, and most advice I've seen is to carry both passports when I have to renew. But it seems that the IO can just pull an electronic visa record in the system by scanning your passport, so it may not be strictly necessary to carry your old passport if you get a passport replacement. Even so, maybe it'd be good practice to carry your old passport with you, but just seems like a nuisance. I'd almost rather have the e-visa to avoid the trouble and worry of losing the old passport.
Are you planning on de-registering AFTER you get the DTV and are staying in Thailand? Then, no, it wouldn't interfere. `You might get a new tax residency depending on where you spend your time after getting a DTV. However, if you are planning to de-register before applying for the DTV (and I don't know why you'd want to), then it probably wouldn't negatively impact you if you apply at the consulates that don't require in-country residency, like Laos, Indonesia, and so on.