Thanks to MAL@U2 for 1080i BD source.
720p 10-bit HEVC + AAC, with FLAC in MKA.

PP (Eps & NC): inverse telecine, vinverse (no use), crop, nr-deband, descale, CRF = 16
PP (Re-encode of Eps and NC): fix color range, CRF = 16
PP (SP): ivtc or decimate, vinverse (no use), fix color range (partially), nr-deband, crop (partially) and descale, CRF = 16 (mini anime), 18 (movie clips), 22 (staff credits)
PP (Re-encode of part of SPs): crop, CRF = 18 (movie clips)

The quality of the BD is terrible, and some of the videos are re-encoded during the encoding. Please read the following notes if you mind the quality or want to report an issue.

Main issues of the source:

1. Issue of interlacing: Some key frames (scene change) are overridden by an interlaced image with the next frame, causing half of the frame data to be missing. Considering the unavoidable deinterlacing issues and the issues of the source, and also considering that (1) I’m inexperienced, (2) interlacing will die and (3) I have never watched this show, I just encoded it conveniently, I decide to leave these issues in the encode and not bother to fix them. So don’t report any combing issue.

2. Issue of colors: After comparing with the web source, I discovered that the video was strongly filtered to enhance the contrast, resulting in better viewing but wiped details in darker parts of the images and too strong colors in some scenes. Regarding the color range, the Y plane is mostly ≥ 16, sometimes a bit > 235, but the U and V planes are totally in PC range, which can only be discovered in some extreme scenes, so I didn’t notice that during the first pass of encode until I started to encode the SPs. To save time and energy, I have to re-encode the videos to fix that. The encode settings are not written for consistency. You can find the CRF values above in the notes.

3. Other issues: The 1080 resolution is by pure upscale (including the text), so descaled to 720p in encoding; the video is noisy, but the artworks are simple so zero denoising still produced low bitrates; line arts has no aliasing and only the text are aliased, so no aa process is done; the SP movie clips are processed and upscaled in an ugly way and hard to fix, so nothing is done. Also the episodes are connected in the discs, which requires extra work.

4. Other notes: The menu of the episodes and NC can not be parsed or converted, so titles of the episodes and chapters are written in the MKV.

In a nutshell, I regret doing this problematic BD pretty much.
Please report major issue only (like corrupted video or wrong audio), issues mentioned above will not be fixed.

I’ll consider encoding Box 2 and 3 as long as MAL upload the BDMVs and as long as I can download them.

(〜￣△￣)〜