I found a partial solution to my question, in that I merge the sperate PDFs in one file. However, this process is very time consuming, and I hope to find a better answer within the Atlas functions.
PdfListe = 
for comp in manager.printLayouts():
for i in range(0, comp.atlas().count()):
Download QGIS and follow the instructions here How can I import a GeoPDF file as a layer in QGIS 3? . It's straight Add Vector Layer. It's incredibly slick; you can choose which layer to import and even import separate label layers.
i have a partial solution...
I know how to do it in QGIS, in atlas tab and then in output check single file export when possible. If you activate this option in your layout and then save you should be able to use it in pyqgis to export atlas in one page (i haven't tried).
If it doesn't work then I try to find the name of the parameter. I have saved two ...
You can open local or online files referenced by relative path or weblink with the attachement widget in QField.
Configuration in QGIS:
You can also add / change pictures in QField. But other file types (like PDF) are currently read only.
Filepaths (local ones or weblinks) in attachement widgets are recognized by QField (at least since 1.9) and available as read-only hyperlinks.
Beeing able to edit them would be a nice enhancement, but is not yet possible.
I believe the solution is move the authentication manager section up in my code to be above the project.read() statement. It needs to be initiated prior to the project being read or any layers with config authentication will have issues.