I don't think I agree, although I suppose it's up for interpretation. You're of course free to mod out things you don't agree with, as always.
In this case, I suppose it is possible to interpret the destruction of planetary population by ship bombardment as "merely" the causing of so much damage that the civilized space age assets there are merely un-useful to their parent empire. That argument has some merit - it may be that "glassing" a planet is just making it effectively need to be rebuilt, rather than necessarily killing all of the millions or billions of defenseless civillians that may be there.
On the other hand, it is perhaps more easy, natural, and common, to interpret this game event literally - that it does represent wholesale extermination of civillians, perhaps even to the point of trying to kill them all or, to use the usual expression on this forum, "glassing" the planet.
The USAF's attacks that levelled German and Japanese cities in World War II were amazingly horrible and killed massive numbers of civillians, but they did not exterminate everyone. In SE4 terms, this could be seen as either literally destroying everything and everyone (what the AI does unless you set Target Planets to False), or as just destroying the facilities and leaving the population (which you could do manually in SE3, but I think in SE4 even a human player isn't shown how many facilities are left, so you couldn't really do that even if you wanted to in SE4, and certainly not in simultanous games where the AI leads the battles).
I don't think it's really possible to interpret the shooting off of all the population units on a planet as not involving massive numbers of massacreing civillians. The good ol' USA may have done this plenty in WW2, but a mere 60 years later, and long before real space expansion, I think the trend is definitely towards recognizing that there may be something just a wee tad evil/horrible/immoral/wrong about mass-slaughtering civillians to get a military advantage.
Anyway, I like to hold out hope that many otherworldly races, and even our depraved species, once they are so advanced that they spread into space, will have developed at least a modicum of morality in these terms.
Moreover, I generally leave Target Planets = True for the Capture Planet strategy, and if this strategy reaches a planet but forgot to bring troops, or other such accidents, the AI will go massacreing civillians anyway.
For the most merciful races, I may even leave their "Capture Planet" strat set to not target planets, though then their AI will need to be tweaked so it has some chance of dropping troops without always getting annihilated by weapon platforms.
All of this brings up the
other main reason why I set this to false in most cases, which is so that ground combat will be more a part of the game. If the AI would just show up and lay waste to planets from orbit, there would be much less ground combat. Given how long it takes (and how expensive it is) to develop a colony in Proportions, this is also, I would think, something of a practical advantage - if the AI conquers enemy colonies rather than bLasting them, it will gain a lot more. Even without transports, though, it may be useful for the AI to sit on enemy planets without attacking - blockading them without getting their ships creamed by the planetary defenses (maybe).
Of course, the AI is needing quite a few tweaks still, including getting more invasion transports out there.
Anyway, those are my thoughts.
PvK