Why would you need to handle $1,000,00 as anything? I'm not aware of any convention that uses the same punctuation mark for both a digits separator AND a radix mark.Personally I use a leading zero to add clarity, but accepting there are other standards I don't obsess.
I don't think I could handle $1,000,00 as $1,000.00. They have two different connotations.
What is most confusing (in both directions) is when you have a number such as
x = 12,345
I see that and see something between twelve thousand and thirteen thousand. In other parts of the world, they see that as something between twelve and thirteen.
Usually, there is enough context (or at least one number somewhere, such as y=12,5) to clue you in to what convention is at play.
This is why the formal style recommendation is to NOT use any punctuation for digit separators and, instead use a space. That way you know that ANY symbol between digits is a radix point. So you would have
$1 000.00
or
$1 000,00
I definitely prefer the leading zero, particularly in handwritten stuff or stuff that is likely to be printed out and used for some time (and subject to dirt and scuffs and such).
That is why the convention started of using the prefix as a radix point so that 4.7kΩ was written as 4k7, while 0.47kΩ was written as k47 and 47kΩ was written as 47k. If there was no prefix, then R was used instead (and C for a capacitor and L for an inductor).