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.
There is no renewal... You exited the Kingdom of Thailand, then re-entered and got a new permission to stay for 180 days. An extension of your permission to stay is when you apply at the immigration office inside Thailand to get another 180 days without leaving the country.