What's wrong with VLC seeking and/or MKV created by ffmpeg?

Question

I have creeated a video using FFmpeg. It is a result of putting 4 videos together, tiled, using -filter_complex with overlays.

Following the how-to here, I have it created as MKV.

When playing this in VLC, the file is sometimes not seekable and sometimes the seeking acts weirdly - it displays some length, but it is only seekable up to the length of the shortest overlay. And the console logs a lot of errors on seeking, like:

VLC media player 3.0.4 Vetinari (revision 3.0.4-0-gf615db6332)
[000055d320ad9630] main libvlc: Running vlc with the default interface. Use 'cvlc' to use vlc without interface.
libva info: VA-API version 1.1.0
libva info: va_getDriverName() returns -1
libva error: va_getDriverName() failed with unknown libva error,driver_name=(null)
[00007f4358002ca0] glconv_vaapi_x11 gl error: vaInitialize: unknown libva error
libva info: VA-API version 1.1.0
libva info: va_getDriverName() returns 0
libva info: Trying to open /usr/lib/x86_64-linux-gnu/dri/i965_drv_video.so
libva info: Found init function __vaDriverInit_1_1
libva info: va_openDriver() returns 0
[00007f43b0c8ccc0] main decoder error: Timestamp conversion failed (delay 300000, buffering 100000, bound 9000000)
[00007f43b0c8ccc0] main decoder error: Could not convert timestamp 33852223320 for FFmpeg
[00007f43b0c8ccc0] main decoder error: buffer deadlock prevented
[00007f43b0c8ccc0] main decoder error: buffer deadlock prevented
[00007f43b0c8ccc0] main decoder error: buffer deadlock prevented
[00007f43b0d69240] main decoder error: Timestamp conversion failed (delay 300000, buffering 100000, bound 3000000)
[00007f43b0d69240] main decoder error: Could not convert timestamp 33862004475 for faad
[00007f43b0c8ccc0] main decoder error: buffer deadlock prevented
[00007f43b0d69240] main decoder error: Timestamp conversion failed for 142272501: no reference clock
[00007f43b0d69240] main decoder error: Could not convert timestamp 0 for faad
[00007f43b0c8ccc0] main decoder error: buffer deadlock prevented
[00007f43b0c8ccc0] main decoder error: Timestamp conversion failed (delay 300000, buffering 100000, bound 9000000)
[00007f43b0c8ccc0] main decoder error: Could not convert timestamp 33884814492 for FFmpeg

Then I created the same video as MP4, and it works fine, except, when the shortest video quarter "ends", the resulting file stops too, and the resulting play time is not accessible (meaning, the position widget is towards the beginning rather at the end). Here are the errors thrown during playback of that MP4:

[00007f8bbc000c40] main input error: ES_OUT_SET_(GROUP_)PCR  is called too late (pts_delay increased to 300 ms)
[h264 @ 0x7f8bfce0a780] co located POCs unavailable
[h264 @ 0x7f8bfce7e160] mmco: unref short failure
[00007f8bbc000c40] main input error: ES_OUT_SET_(GROUP_)PCR  is called too late (pts_delay increased to 755 ms)
[h264 @ 0x7f8bfce0a780] co located POCs unavailable
[h264 @ 0x7f8bfce19f00] mmco: unref short failure
[h264 @ 0x7f8bfce61f80] co located POCs unavailable

All overlays have shortest=1, which should cut the resulting video at the end of the shortest.

What is wrong, and how can I fix that?

ffmpeg version 4.1-static https://johnvansickle.com/ffmpeg/  Copyright (c) 2000-2018 the FFmpeg developers
  built with gcc 6.3.0 (Debian 6.3.0-18+deb9u1) 20170516
  configuration: --enable-gpl --enable-version3 --enable-static --disable-debug --disable-ffplay --disable-indev=sndio --disable-outdev=sndio --cc=gcc-6 --enable-fontconfig --enable-frei0r --enable-gnutls --enable-gray --enable-libaom --enable-libfribidi --enable-libass --enable-libvmaf --enable-libfreetype --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libopenjpeg --enable-librubberband --enable-libsoxr --enable-libspeex --enable-libvorbis --enable-libopus --enable-libtheora --enable-libvidstab --enable-libvo-amrwbenc --enable-libvpx --enable-libwebp --enable-libx264 --enable-libx265 --enable-libxml2 --enable-libxvid --enable-libzimg
  libavutil      56. 22.100 / 56. 22.100
  libavcodec     58. 35.100 / 58. 35.100
  libavformat    58. 20.100 / 58. 20.100
  libavdevice    58.  5.100 / 58.  5.100
  libavfilter     7. 40.101 /  7. 40.101
  libswscale      5.  3.100 /  5.  3.100
  libswresample   3.  3.100 /  3.  3.100
  libpostproc    55.  3.100 / 55.  3.100

The full command to get the video is, for instance:

ffmpeg \
 -i '/.../2014-11-21/....mp4' \
 -i '/.../2016-01/....mp4' \
-filter_complex "nullsrc=size=960x270 [lay0];
      [0:v] setpts=PTS-STARTPTS, scale=480x270 [TILE_1_1]; 
      [1:v] setpts=PTS-STARTPTS, scale=480x270 [TILE_1_2]; 
      [lay0][TILE_1_1] overlay=shortest=1:x=0:y=0 [lay1]; 
      [lay1][TILE_1_2] overlay=shortest=1:x=480:y=0     "      -c:v libx264 ./tiled.mp4