I partially agree. I don't belong to the perfectionists for whom the slightest flaw already puts an end to the implementation of an idea; in other words, I would implement (and will implement) any technically feasible ideas, even if they have some problems (of course, if these problems are not critical). Of course, there will be those who think otherwise, so, in my opinion, the possibility of such a unit appearing in very rare cases, as a boss-easter egg, is quite justified.
As an example, I think you are well familiar with NHF and the fact that some awkwardly or not very conveniently implemented moments there (for example, special units like Hafad) have explanations and caveats that clearly let the player know that these are technical problems of the game, and not flaws of the author. Well, I think the analogy is clear.
It seems to me that everything here strongly depends on the criticality of the bug and the interestingness of the feature.
For example, creatures running through another creature, as I think, is a very critical bug for the sake of the feature of a 3x3 creature.
On the other hand, there was an idea to make alternative buildings in cities so that it would be possible to recruit not 7 creatures with upgrades, but 14. So, this is also feasible with bugs. The city level will increase by 2-3 points for some buildings. And in order for some creatures to appear in the recruitment window from the city, you will need to exit and re-enter. But, in my opinion, these bugs are worth the feature, and they can be written about in the description of a specific building. The bug with the city level can even be played out in the gameplay.
Added 5 minutes ago
Do all creatures run through? Or only allied/enemy ones? And can creatures stay in the 3x3 area (I think not, because you can't direct a turn specifically into this area)? The arrangement can be fixed, although it is not easy, and if you use the Kraken as a solo boss, there will be no problem at all... but in general, yes, there are too many unnecessary conditions for a mod on visuals, so I will leave the idea for single-player.
I can't say for sure, it seems like all of them. This happens rarely; the creature must have a direct path past the "extra" cells of the 3x3 creature. You can't direct it, yes. But, as I said, when arranging, the AI places its creatures "inside the 3x3 creature." A solo boss seems too boring to me. Well, okay then)) This mod is not entirely focused on visuals; I still try to integrate the creatures normally into the game. So, there is some gameplay here.
And by the way, if you make it so that the Kraken boss drops only once out of 3 times, then why is it needed at all? I mean, the flooded Temple itself is a rare building on the maps, and here you have further reduced the player's chances of encountering this Kraken boss.