Yes the promoted properties cannot be changed in SharePoint they just display what is in the form.
Now does the Workflow ID and other fields get assigned in the form? Or do you want them to be modified by some external process? You are pretty much stuck editing these fields within the form.
OK, I just had one idea, have not tried it, but I will write it out and see if it makes sense. I am thinking it would be possible to create a seperate SharePoint list, which could be modified and then just have one of the fields contain the link to the corresponding form in your form library. To create the link should not be hard since the path is constant and you are creating the name the form is saved under. You can use a CAML and update the SharePoint list as the form is submitted, a tutorial is in a blog here. This might give you the functionality you are looking for and the user would have a hyperlink that would behave the same as selecting the form in the form library. You could filter the list if you wanted and also use it as a secondary data connection to update the form when it was opened to the new values that were possibly set in SharePoint.
So form is created and submitted. Submit saves it into the form library, the SP list is inserted with a new row that contains the fields you want and a hyperlink to the form.
Someone in SharePoint updates the list values. Then they or someone else uses the hyperlink and opens the form. As the form opens it checks the values of the SP List and updates its values to match. The user sees the form with the values set in SharePoint. I believe this is what you are looking for.
Typically any values that pertain to the form are changed in the form and SharePoint just allows you to see some key fields before you open one. But I believe in this scenario, although somewhat complex, could allow for fields in SharePoint to be used in your forms and modified externally, at least from the users perspective.
Not sure if this what you need but I am trying to be creative. :)