This is not going to be super-intuitive, but instead of the Numbers effect, you can use a Text layer, an Angle control (because sliders don’t go to 1 billion), and an expression.
1. Add a text layer.
2. Add an Angle Control effect to the text layer.
3. Keyframe 0 and 1000000000 as you like on the Angle Control.
4. Untwirl the text layer, then Alt+click the Text > Text Source stopwatch.
5. Enter this expression:
var numberAsText = "" + parseInt(effect("Angle Control")("Angle"));
var separator = ",";
numberAsText.replace(/\B(?=(\d{3})+(?!\d))/g, separator);
The first line gets the value from the angle slider as an integer and changes it to text. The second line says we’ll use a comma as the separator, i.e. so you get 1,000 instead of 1000. (If you don’t want a separator, you can clear out the comma, leaving nothing between the two quote marks. If you want to use a period, change the comma to a period.) The third line is a little crazy, but it uses something called a regular expression to insert the separator every three digits, starting at the end.
Here’s a project with all this set up so you can see.