I see the issue, and the thought had crossed my mind earlier. I agree it could definitely be an undesirable side-effects.

Off the top of my head, one solution I see is to build a default content formatter property for each identify layer in the identify widget.

function getContentFormatter(args){
  return function(attributes){
    // getFormattedAttributes will return the attributes and apply any formatters
    // it can also remove properties that have `include: false` or we could implement 
    formattedAttributes = getFormattedAttributes(lang.clone(attributes), args.fieldInfos);

    //getTableHtml will iterate through the attributes and create table html
    return getTableHtml(formattedAttributes);
  }
}

and then

popup.setContent(getContentFormatter(this.identifies[layerid][sublayer_id]))

I don't think there's really a great solution to this that doesn't result in a lot of redundancy. The solution I mentioned above wouldn't work well since we'd have to replicate the functionality of the popup parts when there is no content function (title, fieldInfos, attachments, etc...)

Another solution would be to put the original cloned attributes in an extra property like feature.originalAttributes but I don't see the real benefit there since we're renaming the property and much of the api that would use the attributes property anyways.

Perhaps the best solution is to warn people, and if they need the original value, create instead a virtual field with a formatter and exclude the other field from the identify popup.

@roemhildtg I agree. Using virtual fields with a formatter is how I work around this and it meets all my requirements so far. I think some info in the docs alerting folks to the potential pitfalls is the way to go.