Per episode... I used the 3d denoiser at low setting, which helped a lot. I know Seasons 1-2 are really bad in terms of quality, which is why I mentioned it.. suspecting that s1-2 will be closer to the larger sizes because of it.

How would I use a 3d denoiser with ffmpeg? Any tips?

The filter hqdn3d is what you want. Note that the defaults are for noisy video, so unless you have a really noisy source you'll want to use lower settings. I've seen hqdn3d=4:4:3:3 as a good place to start, and you can tune the numbers (lower is more noise, less blur, higher is less noise, more blur). In addition, the default values for each parameter is scaled based upon the previous value(s), so you can be lazy and just pass one or two values to get a coarse idea of the strength you want.

If the videos are to be played back on a player that supports video filters, you can add some noise back in on decode, which is particularly useful for non-HD sources as your eyes will often interpret noise as detail. Back in the h.263 days I used to do this as 1) h.263 was much worse than 264 or 265 and handling noise and 2) disk space was more expensive, so I couldn't just up the bitrate. I still have some vlc settings that can do that for playing old DVD rips. Today, unless you plan on streaming the video, I would recommend just upping the bitrate and using conservative enough denoise settings to not need it.