If I were to add an extra "tag" for foldingStartMarker and foldingStopMarker in the PHP bundle, am I under the assumption that it would be read by the HTML bundle when TextMate sees it inside the <?php ?> region?
When I am editing a PHP file and set the bundle to PHP, the folding marks show up. But, when in HTML mode and use the same markers in the PHP region, the folding marks are no longer appearing.
No only the folding markers from the main language are used. To get what you want you need to add them to the HTML grammar.