The rule is that the the amount of the check written out in words takes precedence over the amount that is written in figures (numbers).
Theoretically, this means that OCR reads the amount in written words only. Or perhaps both are read to develop some level of confidence that the amount written out in words was properly read.
It's possible that some ATMs only read the amount written out in numbers (which is technically incorrect), but keep in mind that any/all data read by the ATM are subject to review.
In my experience, after the ATM scans the check, and "Reads" the check amount, you are shown (on screen) the amount it has read and asked if it is correct. If you answer "No", you would be allowed to manually enter the "Correct" amount.
The point is, that at a later time, a person will verify that the amount was correctly read from the amount written in words. For the amount that is written in numbers, it can be in any of the forms you have suggested, or others which may or may not be readable, or perhaps even not present (blank)... basically, it is not relevant in determining the amount of the check.
As far as your other question about including the "Thousands separator"...
I always include it, but I also include the "Cents" amount even if it was zero (.00), so I would write it out in numbers (here in the US) as
1,234.00. But, as I said above, this amount is not used in determining the amount that will be paid for the check.