Hi again!
Unfortunately I didn't include any endgame quests, I was working on an extensive line of sub-quests with the story behind every mercenary (like understanding their background and learning new abilities), but decided to release the game with just the main story, as it already had a lot to offer and the system I was designing for them was way too complex for my current skills given that it's my first game (in case you were wondering, it was a trait system with 80+ talents and gathering/crafting system with hundreds of materials and recipes that were spread around the whole world).
I totally forgot to remove the NPC with the Galaxy Comprehension Items, which was part of the abovementioned subquests (for Seyth). The Runesmith was part of these quests too (for Hyo).
The Trading Cards were part of a removed side quest indeed, I kept the items in case I wanted to include it again, which wasn't the case.
As for the Desert Field 03 chest... I misplaced that chest, I will move that to fix it in a new update.
And as for the Monster Codex: All of them can be encountered, the first two you mention are both actually pretty common mobs in the Lost Tomb (30%), they appear together. I'm impressed you didn't encounter them when solving the puzzle!
The last monster has a low spawn rate (5-7%) in 2 of the 4 fields in Antalaya and drops some nice loot :)
I'm very grateful for your thorough gameplay and I appreciate all the pointers on the details I missed, I'll be sure to fix them up :)