Upscaling by a non-integer ratio without filtering will always cause scaling artefacts.
Maybe VC just use some different filtering method, who knows?
Also try to force emulator video mode to progressive (480p), i think interlaced video can also cause scrolling artefacts like that because the original 240p picture is rendered at 60fps then upscaled to 480i and displayed at 30fps which causes flickering. Some emulators have a separate deflickering filter to fix that. Bilinear filtering is generally what causes the blurry output, not deflickering.
I don't know what the FILTERED option in FCEUGX does exactly but you should at least try if it fixes your issue before deciding you "hate" it...