No expert here, but it sounds like a quirck related to your display. What TV/monitor are you using? Any chance you can rectify the wrong aspect ratio, by acting directly via its settings?
I only used PC monitors (1080p and 4K) with the OSSC, so far, and had no problems with them detecting the correct aspect in 480i>bob (both in Line2x and 4x). No luck getting Line3x displaying anything on the 1080p ones – my 4K LG did, though – and I can confirm Passthrough messes things up real bad on all of them (stretching to fullscreen no matter what, and generally producing a pretty awful PQ, due to poor scaling capabilities).