The SSIM values calculated using FFMPEG are not what I expected - ffmpeg

Question

I'm trying to encode an m2ts (MPEG-2 Transport Stream) file to mp4 (H.264) and get the ssim value.
I did get some SSIM values, but the results were contrary to my expectations.
Are there wrong command options for ffmpeg?
Encoding and SSIM calculation commands
# encode
$ ffmpeg -hide_banner -fflags +discardcorrupt -i input.m2ts \
-c:v libx264 -crf <CRF> -preset:v medium \
-c:a copy -bsf:a aac_adtstoasc \
output_ff_crf-<CRF>.mp4
# calculate ssim
$ ffmpeg -hide_banner -i <A> -i <B> \
-lavfi "[0:v]settb=AVTB,setpts=PTS-STARTPTS[main];[1:v]settb=AVTB,setpts=PTS-STARTPTS[ref];[main][ref]ssim" \
-f null -
The results of the SSIM
(a) A=input.m2ts, B=input.m2ts, ssim=0.973266
(b) A=input.m2ts, B=output_ff_crf-0.mp4, ssim=0.813347
(c) A=input.m2ts, B=output_ff_crf-30.mp4, ssim=0.819897
(d) A=output_ff_crf-0.mp4, B=output_ff_crf-0.mp4, ssim=1.000000
(e) A=output_ff_crf-0.mp4, B=output_ff_crf-30.mp4, ssim=0.972911
(d)(e): These are what I expected.
(a): The files are the same, but ssim≠1.
(b)(c): SSIMs with CRF=0 and CRF=30 have almost the same value, although the image quality is different.
In the case of HandBrakeCLI
To determine if there was a problem with input.m2ts, I ran HandBrakeCLI with almost the same parameters as ffmpeg.
# encode
HandBrakeCLI --verbose --format av_mp4 --encoder x264 --quality <CRF> --x264-preset medium \
--aencoder copy \
--input input.m2ts --output output_hb_crf-<CRF>.mp4
# calculate ssim (same as ffmpeg)
$ ffmpeg -hide_banner -i <A> -i <B> \
-lavfi "[0:v]settb=AVTB,setpts=PTS-STARTPTS[main];[1:v]settb=AVTB,setpts=PTS-STARTPTS[ref];[main][ref]ssim" \
-f null -
(b') A=input.m2ts, B=output_hb_crf-0.mp4, ssim=0.999999
(c') A=input.m2ts, B=output_hb_crf-30.mp4, ssim=0.972886
(d') A=output_hb_crf-0.mp4, B=output_hb_crf-0.mp4, ssim=1.000000
(e') A=output_hb_crf-0.mp4, B=output_hb_crf-30.mp4, ssim=0.972886
It's all as I expected. (although A is not ssim=1.0)
Therefore, I don't see a problem with input.m2ts.
Informations about video files and tools
Results of the ffprobe
input.m2ts
[mpeg2video # 0x5655577c1680] Invalid frame dimensions 0x0.
Last message repeated 1 times
[mpegts # 0x5655577bd080] start time for stream 2 is not set in estimate_timings_from_pts
[mpegts # 0x5655577bd080] PES packet size mismatch
Input #0, mpegts, from 'input.m2ts':
Duration: 00:30:02.68, start: 39593.392600, bitrate: 19019 kb/s
Program 211
Stream #0:0[0x140]: Video: mpeg2video (Main) ([2][0][0][0] / 0x0002), yuv420p(tv, bt709, top first), 1920x1080 [SAR 1:1 DAR 16:9], 29.97 fps, 29.97 tbr, 90k tbn, 59.94 tbc
Stream #0:1[0x141]: Audio: aac (LC) ([15][0][0][0] / 0x000F), 48000 Hz, stereo, fltp, 255 kb/s
Stream #0:2[0x138]: Data: bin_data ([6][0][0][0] / 0x0006)
Unsupported codec with id 100359 for input stream 2
output_ff_crf-0.mp4
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'output_ff_crf-0.mp4':
Metadata:
major_brand : isom
minor_version : 512
compatible_brands: isomiso2avc1mp41
encoder : Lavf57.83.100
Duration: 00:30:02.67, start: 0.000000, bitrate: 109301 kb/s
Stream #0:0(und): Video: h264 (High 4:4:4 Predictive) (avc1 / 0x31637661), yuv420p, 1920x1080 [SAR 1:1 DAR 16:9], 109040 kb/s, 29.97 fps, 29.97 tbr, 30k tbn, 59.94 tbc (default)
Metadata:
handler_name : VideoHandler
Stream #0:1(und): Audio: aac (LC) (mp4a / 0x6134706D), 48000 Hz, stereo, fltp, 252 kb/s (default)
Metadata:
handler_name : SoundHandler
output_hb_crf-0.mp4
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'output_hb_crf-0.mp4':
Metadata:
major_brand : mp42
minor_version : 512
compatible_brands: isomiso2avc1mp41
creation_time : 2020-05-17T06:22:06.000000Z
encoder : HandBrake 1.1.0 2018042400
Duration: 00:30:02.22, start: 0.000000, bitrate: 109661 kb/s
Stream #0:0(und): Video: h264 (High 4:4:4 Predictive) (avc1 / 0x31637661), yuv420p(tv, bt709), 1920x1080 [SAR 1:1 DAR 16:9], 109405 kb/s, 29.97 fps, 29.97 tbr, 90k tbn, 180k tbc (default)
Metadata:
creation_time : 2020-05-17T06:22:06.000000Z
handler_name : VideoHandler
Stream #0:1(und): Audio: aac (LC) (mp4a / 0x6134706D), 48000 Hz, stereo, fltp, 252 kb/s (default)
Metadata:
creation_time : 2020-05-17T06:22:06.000000Z
handler_name : Stereo
Tools
version
ffmpeg: 3.4.6-0ubuntu0.18.04.1
HandBrakeCLI: 1.1.0
ldd
$ ldd /usr/bin/ffmpeg
...
libx264.so.152 => /usr/lib/x86_64-linux-gnu/libx264.so.152 (0x00007efbf1f33000)
...
$ ldd /usr/bin/HandBrakeCLI
...
libx264.so.152 => /usr/lib/x86_64-linux-gnu/libx264.so.152 (0x00007efbfb38f000)
...
ffmpeg and HandBrakeCLI are using the same libx264.