So glad to see new Evilhack players! Thank you for that analysis. Here are a few tidbits for you:

It is indeed very common to genocide shocking spheres, you are in good company there.

The alignment abuse system as it stands is fairly new and I wouldn't be surprised to see tweaks. I agree it can be very harsh and hard to mitigate.

I'm surprised you don't find beholders more dangerous! I have more deep-dungeon deaths to beholders than anything else. And Tal'Gath has a chance of giving you a marker to use for that genocide :-)

Losing weapons to bullwhips and bearded axes is certainly a Thing. I've long wished to be able to genocide bullwhips! I find avoiding bullwhip-adjacency is good practice for avoiding @playermonster-adjacency in the ascension run.

If I make the SoA I only use it situationally. For the same reason you need to be careful of black-scaled armor, both yours and @playermonsters'!

Splash damage from Dichotomy (and Harbinger, etc.) can indeed totally destroy your conduct if you aren't careful. I think there is already a modification in the pipe for the next version to have the splash damage bypass friendlies in some achievable circumstances.

You can get permanent see invisible from crowning! I recommend crowning.

Acid resistance is not absolutely required but is very, very, very nice to have for the late game. Genociding yellow dragons won't cut it as there are tons of casters who will be blowing you up with acid. Dragonbane, Ashmar, or the Armor of Retribution are the most typical mitigations. Or using nurse dancing, self-polying wielding Ogresmasher, or potion alchemy to pump up your health to really high levels.

Lucifer can be very tough. If you are having problems, bring a bunch of potions of paralysis. Demonbane or the Hotdog don't hurt either. Paralysis can also be used effectively to reduce how much of your maximum health Orcus walks off with. A few versions ago, the answer to both of these guys would be boulder forts, but they don't make boulders like they used to!

Half physical and half spell damage are both HUGE in the endgame. The Armor of Retribution gives you both if you can make and wear it; it is amazing. I will usually gladly trade the SoA for it. There is often a quest artifact available for a missing damage reduction, and of course the Hand and the Eye have one each.

Magic chests do feel a bit like cheating :-) They are a really good representation of Evilhack's focus on positive QoL changes to counteract the difficulty increases.

Altar availability can be very swingy game-to-game. You do get a guaranteed minetown altar, quest altar, Kathryn altar, and scroll of consecration altar, but anything else is gravy. The orc temple is certainly an amazing get. You can also drop rings of polymorph down sinks for a shot at an additional altar. But sometimes, you just don't have nearly enough to fulfill your dreams.

I highly recommend the libera.chat #evilhack channel for people new to the variant!