In a Document with Revit links: sectionbox is graphically overridden by some other sectionbox when applying view template.

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Hello everyone,
I have a Revit file with linked models. using the API I (1)generate 3D views & (2)set a sectionbox. everything comes out fine.
but if between steps (1) and (2) i assigned a view template to the view, the view template overrides the sectionbox assigned by which graphically the sectionbox is different than the set section box value assigned.
Any help with this is very much appreciated. How can a view template affect something such as the visible drawn section box.
attached: how a bigger than assigned sectionbox is drawn is shown in the screenshot, the snooped value & how the outcome would be if no template was used.
note that I isolate the elements am interested in while creating the view as well as permanently isolating them, I wonder why the levels are shown in the back?