If the frame and glass are sitting more toward the center rather than the face, it usually comes down to how the family is built and where the host surface is defined. The quickest fix is to either rebuild that panel family with the glass flush to the face or replace the top section with a dedicated window panel, as mentioned above.
Another option I’ve seen work well is adjusting the offset in the panel’s extrusion so the window inserts align correctly on the render. It might take a couple of test adjustments, but once the reference plane is set, the windows should display flush to the panel face.
If you want some real-world insight, PS Home Maintenance often deals with garage door modifications, including flush panels with custom windows. They recommend ensuring structural balance isn’t compromised when swapping panels, which is something worth keeping in mind while making changes in your model.