You only report when you have been in Thailand for 90 consecutive days. If you leave before 90 days, you don’t need to report and when you come back in, the timer starts back at day 1.
In regards to your health issue, did you submit the treatment plan with booked appointments or did you focus on past appointments? Did you have the hospital write you a letter?
From their perspective, it looks like you were trying to apply as a digital nomad with paperwork for a company that no longer exists. You only informed them of this when they asked for additional documentation. I could see that as being a major red flag for them. In regards to Vietnam, each embassy has their own requirements. However, it is a central system so your rejection might make it harder to apply in other locations