I'm trying to fix the issues you detailed. I'll try to answer what I can first:
Can't carry potions. They are rune types. Mana spam but not health?
There's only 1 non-powerup potion type in this map (Potion of Health). Otherwise, health is restored instantly when you kill an enemy. Mana is restored through powerups.
You can use the Senior Guard's summoned troops to farm for XP.
Technically, it's possible, if you are good enough at kiting with early game's health and mana.
What have I missed? "A feeling of emptiness [...] as if something has gone by and you missed it".
Just a secret. It's not gonna affect the story or gameplay.
No mana during challenges? Challenges are pretty much attack+move.
Yeah... I sort of make them similar to dream-like trances where you can't cast spells and have to blast your way through with brawling. It's just a way to farm up developer's comments (which counts toward a secret)
Those skeletal orcs are too powerful/many (way gate corridor), immune to magic too. Not sure how mages will deal with them as it's already almost impossible with the templar. Lucky I could beat them standing in a corner using the ultimate with the Lightning bonus.
Yeah, I intended it to be so. You should stand in the corner to minimize the number of creeps hitting you, since they are magic immune.
Every time I load the game, undead summon building sounds can be heard.
I don't have this problem. Perhaps it has something to do with special effect animations (though I checked meticulously to prevent leaks).
After "freeing" Abaloth, the unit remains in its channeling animation, it still has no attack and just text messages the player: "Taste this!" and after a while "Burn!". The order in which the souls have been killed, the one in the southeast, the one in the northeast and lastly the one in the northwest. Maybe, the boss was supposed to summon units via triggers or somehow/something?
You just have to attack him. He's the boss after all.
Loading the game where the blue and red lightning lines are will crash the game if you go into their zones.
Yeah that is definitely very annoying, since I really wanted to create a lightning trap system and also want to prevent leaks without making the game crash.
That purge spell

eliminates the Lightning Shield on the Burkards fast. Then, it's easy to get them into a corner where they can't attack anymore.
I'm sure the Lightning Shield is just visual FX to alert to you that they're about to throw their big buzzsaws.
I see no rock. Was there supposed to be one in the cell's southwestern corner but the model doesn't show? Yep, that's why. Even in the editor they show as no model green blocks.
Then this is definitely a very annoying issue. I originally used a hidden model "Doodads\Terrain\G_RockChunks\G_RockChunks" for those rocks, but in 1.31, that model is no longer included in the data, so I extracted the model and imported them as custom models. They show up properly in my game, I don't know why they don't in yours, looks like I'll have to use the default Rock Chunks model for safety.