A program for calculating the strength of the guard on random maps in Heroes of Might and Magic III, called H3CalcGuards.

Further, how to explain the facts of generating 2 stables or 2 lookout towers on one respawn? I understand it's a generator bug, because I've seen outright doubling on the respawn. I.e., guards of 2 nagas or 2 imps or Dragon Utopias almost on top of each other.

Yes, it's a bug. The issue is that when the generator forms a group of objects, it does not account for the fact that objects already added to the current group (but not yet placed on the map) also need to be counted in the quantity. Because of this, 2 lookout towers, stables, and the like can be generated on a respawn - but always in 1 group.
Theoretically, this bug can have critical consequences. For example, if this causes more than 32 experience stones to be generated, then when visiting the 33rd experience stone, some other object will be marked as visited by the hero, or the information will generally become corrupted.

Further about the pickups. It turns out that, using the same Jebus Cross as an example, if there is an additional zone with your respawn, the guards of the pickups increase incredibly? Practically doubled. 1/5 and 2/5

Well, the resulting value coefficient without the extra respawn is 1 + 1/5 + 1/2 = 1.7; and with the extra respawn is 1 + 2/5 + 2/2 = 2.4.
That is, still not doubled, but almost one and a half times as much.
True, this doesn't necessarily mean the guards will also increase by one and a half times, since the relationship isn't directly proportional (here I wrote about how guard strength is derived from value, if you're interested: http://forum.df2.ru/index.php?s=&showtopic=27998&view=findpost&p=558697).