The issue, if I understand correctly, is about inheritance - specifically of Key Attributes (KA, as stored in $KeyAttributes). Any note that has $URL set and made a KA as a result of drag-drop now has locally set $KeyAttributes and therefore cannot inherit a newly assigned prototype's KAs: local settings trump inherited ones.
If a link is dragged from a Safari web page into Tinderbox in v6 or v7, the URL's anchor text forms $Name, and the URL's value is added to $Text. In v7 only the URL value is also added to $URL and set as a KA. If a page's URL is dragged from the location bar the same happens in each case except the page's
<title> string is used for $Name.
So, there's no bug here, inheritance is working correctly. As remains the case, if you set a prototype (that uses particular KA) onto a note with KA already set, you must reset $KeyAttributes to remove the local value and allow inheritance.
In your case, the simplest approach would be to add a stamp (Code:
$KeyAttributes) to reset KA. You could then set your prototype and with the same selection apply the stamp in case any items have pre-exiting local KAs.
The new v7 handling of URL drops is, in the round, more useful for general browser interaction so I think it unlikely this would chance. Note this setting of $URL as a KA occurs only for new notes made via drag-/drop.