Any particular reason you used
--partitions none ?
Using that certainly doesn't help, particularly on the second pass. Use the default setting instead.
Also, why use vfr for output ? That's really looking for extra trouble since static frames barely take up any space at all (x264 marks the static parts of the picture as "skip" and doesn't even encode them). You can easily fit a clean 25min anime episode unresized (720x576 anamorphic, or 720x480 anamorphic) on 175MB and still get acceptable quality (though what's "acceptable" is very subjective).
When I say "clean", I mean correctly denoised. Try adding hqdn3d(2,2,2) just before the resizing step to your script (you'll need the hqdn3d plugin), since DVD's all have noise, even anime ones (and the video you posted is full of noise). If that isn't enough, try hqdn3d() on default settings or fft3dfilter() on default settings instead (much slower).
(I'll let you google the pages for those 2 filters, they're easy to find
).
Also, what you posted isn't as awful as I first imagined. Also, why disable psy-rd ? Was it worse with it enabled ?