It's been a minute since I asked this, but still valid. Lemme explain:
When you use a SEND A NOTIFICATION block in a workflow, you can insert references into the body text of the notification email. One of these references you can insert is to an item's URL - a link that will take the user directly to the item in the list that the notification speaks of.
Is there any option to manipulate or edit the actual URL that the link points to?
It sounds to me like you are using the Common Context Item URL, but you can include any URL in the address, you don't have to use the Reference field. I use variables to create links to specific views in list/library. Insert Link allows you to build the desired link, using whatever address and text you want to use, including fixed URL address, variables, and references. Is that what you meant?
Attached are some examples of URL variables I have used in Send Notification and Task Notification emails.