Hi Lindsay King ,
I assume that the HTML formatting that can be used in ArcGIS Pro, will also be possible in AGOL, since it does not make sense that this formatting disappears when you publish it to AGOL. I do not know when this will be available. There is a big update of the web map coming very soon, but it might not include this feature yet.
You can format the pop-up applying colors, but this will probably require multiple expressions. Can you provide a visual example of what you want to achieve?