So your legal residence is in the EU? That might be the issue, not sure if the Royal Thai embassy and consulates in the US insist on being a resident in order to apply there. That would be the case in the EU though.
If it's not the case, then you could write a cover letter explaining that you are a EU resident, and provide evidence of that.
I don't think being paid in crypto currencies is that much of an issue, as long as you change your income into fiat. You would have invoices with your wallet address, proof of payment to that wallet on the blockchain and proof of exchanging the amounts into fiat through an exchange + transactions going into your bank account. However, having only 2 months income history will possibly be an issue.
Das wird leider nicht hinhauen. Der Arbeitgeber muss in einer Bescheinigung ausdrücklich bestätigen, dass der Antragsteller in Thailand arbeiten darf. Wenn in der Bescheinigung bzw. im Arbeitsvertrag nur Fernarbeit im Allgemeinen erwähnt wird, genügt es in der Regel nicht, aber man kann es evtl. versuchen. Ganz ohne wird der Antrag höchstwahrscheinlich abgelehnt.
We don't know for sure how long she had been in Thailand for, but you're right, it was likely already time to do a new TM.47 and she could have done it at the same time.