HTML is really just "content" so there's nothing you can do with pure HTML that would add the comma separators to the content (i.e., generally speaking, HTML is the content layer, CSS is the style layer, and JavaScript is the functionality layer).

You might want to consider sending the emails via Workflow. You can pull the required information in with Retrieve Business Process Variables, and Workflow has token formatting options that would allow you to format the content with the comma separators.

It's important to note that the source token value must be numeric, so you should add the $ with the formatting; including it in the source value will cause it to be "text" so it wouldn't apply numeric formatting.

Token Formatting--Numeric (laserfiche.com)