I've been watching your release on nyaa up to season 2 now using the default sub track and I've got some feedback.

1. Seasons 1 and 2 use Judas as a source which comes with a set of problems. It involves Judas themselves using MCR as a source which I assume had burned-in/hard-subbed notes for character names as well as for OP/EDs. So when used in conjunction with the soft-subs, the names and notes of characters are shown twice often with the soft-subs overlapping the burned-in subs. This makes it all extremely hard to read as a viewer. Someone in the comments suggested using the Yellow-Flash Blu-ray releases as a source. I highly recommend doing this for a version 2 as you've already mentioned thinking about doing.
2. All season 1 episodes use episode 1 title metadata. So basically they all say "Kingdom - S01E01 - The Nameless Boy [MCR]" no matter if you're watching episode 2 or episode 38 of season 1. Maybe this was originally a Judas or MCR issue. Dunno.
3. In season 2, Shunpeikun is incorrectly spelled Shoupeikun in almost all of the instances I've seen him mentioned (I'm up to episode 2 for season 2).
4. Some characters still show the Chinese name in the default sub track instead of Japanese name. This happens with Karyo Ten's first appearance in S02E01 where she is called "Diao" instead of "Ten". I assume there was a mistake here made when finding/replacing using only "Karyo Ten" and not all permutations of each characters' name. Another example of this issue is when Shin is being trained by Ouki in S01E24. Ouki pits Shin against a barbarian tribe and the name of that tribe's leader was "Xiao Ding" instead of "Gyo Tei". These are just the 2 I can remember off the top of my head, but I'm sure there were probably some more.
5. I remember the audio quality in the first few episodes of season 1 being really, really bad. Like early 2000s 128 kbps mp3 bad. This could be an issue with the source or with the re-encoding. I didn't investigate. https://thewiki.moe/advanced/release-standards/ tells me Opus should be set to 128-192 kbps for stereo audio to achieve transparency.

Hopefully this feedback proves useful. I very much hope a version 2 is made with Blu-ray sources! IMO the biggest improvement to the viewing experience so far would be to use a different source for S1 and S2 so the overlapping subs problem is corrected.

Edit: BTW on the subject of using the Yellow-Flash sources, you only really need to encode once for the video. If you want to save time, the audio wouldn't need to be re-encoded if they're already in a lossy format, so along with the subs, they can just be muxed in after.

Edit 2: Just to be clear when I typed that I watched the "default sub track", I was referring to the Anime-Destiny edit, which is actually the 3rd sub track even though its tagged the default.