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The OSSC will choose the 640×400 preset for 720×400 so you should set H.active to 720 and tweak H.backporch.
It looks like the 640×480 capture is just shifted to the top left a bit. Tweaking H.backporch and V.backporch should shift the image. If it doesn’t then you need a new capture device.
BTW for the sharpest capture you should always set the capture resolution to match the OSSC’s output. Then right click the capture device and change Scale filtering to point and then choose Transform->Edit transform to set the size for the maximum integer scale to fit the canvas. With 640×480 in a 1920×1080 canvas thats 1280×960. Then choose Transform->Center to Screen.
Using LineX2 for 640×480 so the OSSC will output 1280×960 will probably be better quality than passthrough with your capture device because it is set to YUV 4:2:2.
OBS is scaling the preview to fit the window so you should either set Preview scaling to canvas (cropped if too big) or set preview to full screen if you want to see the preview 1:1.