I think some very important points are being missed here. One thing you need to understand is that in most cases you are dealing with false gods who are either creating or co-opting a mythology for their own ends. Kefka was semi-omnipotent but he was a mortal who gained power. "Final Fantasy X" was based loosely around Roger Zelazny's "Lord Of Light" where the church was developed using high technology, with the stated goal of preventing the advancement of technology "until people were ready for it" (which would never come or be accepted due to the status quo serving the controlling elite). In the case of "Final Fantasy X" in particular it should be noted that there actually WAS an apocalypse caused by high technology and the current social order was created to prevent that from happening again.
One thing that should be noted is that in Final Fantasy, ultimately the REAL divine beings play some role in the downfall of the pretenders. This can be as subtle as using white magic, invoking "holy" abilities which for whatever reason the so called "god" isn't granting and thus can't shut down to prevent them from being used against him. Indeed so called White, or Holy magic (oftentimes with a spell called "Holy") is usually required to be used, and used correctly, to defeat a lot of the final battles. But more so than that, consider in the "damning" "Final Fantasy X" Tidus himself pretty much doesn't exist, he's a creation of The Fayth with the specific goal of throwing down the order being talked about here. You more or less have the equivalent of god, turning on the pope, with Tidus being a manifestation of power (sort of like one can argue Jesus as an extension of god). Later games in the series deal with the question of the soul, as the series which is inspired by Lord Of Light uses the same basic technology including a sort of "soul battery" where the spirits of the dead are stored (in Lord Of Light they go futher with it though, tying it to a brain transfer technology that reincarnates people into different bodies, in Lord Of Light the pretenders have assumed the guise of Hindu deities... think of it as transhumanism being exploited in the guise of religion), one of the later plot threads deals specifically with the question as to whether the Tidus you knew (rather than the very different man he was based on) actually had a soul or was merely an extension of divine power... a power which had moved on and left humanity to it's own devices.
In "Final Fantasy 7" the religious connotations are among the most obvious. I think probably more people of my generation learned what "Sepiroth", "Jenovah", and about things like the "Tree Of Life" due to being interested in that game than from any other source. However in this game it's important to note that ALL of this is turned on it's head in the last act. Basically you have "Holy" (God/Good) being invoked to protect earth from Meteor (The Devil/Evil, also sort of based on the mythology of Tiamat and the actual meteor), but it happens too late because humanity had basically turned it's back on religion, and indeed the bad guys were sucking up the very power, running a literal power company, that would eventually be needed to save everyone. What's more the acts of man to save itself, via things like trying to fire a missile at Meteor, fail... basically the real "God" everyone has forsaken is the only answer. The ending of the game pretty much has Holy stepping in to try and save the world, but it's pointed out that due to the stupidity of humanity it's too late, and the devestation is massive. The ending of the game makes it questionable who survived and who did not. Indeed, while contradicted by sequels, it could be argued that originally humanity was deemed unworthy and was pretty much erased, and Red's people inherited the earth. Of course "Advent Children" defined things a little differently, but it should be noted that it literally involves the hero finding peace by briefly visiting heaven before being sent back to the mortal plane.
Now granted, different games have different overall logics behind them, but I do not think you can argue any kind of real "universal" message behind the series. Unless of course it's basically that organized religion and the mechinations of man take us away from the divine and the actual truth. It seems most accurate to say that it's anti-organized religion, as they tend to produce false gods. In "Final Fantasy 7" though it seems that the message has religions connotations but ultimately seems to be anti-corporate, and perhaps anti-technology. On a lot of levels it's like that "Insane Clown Posse" song "Miracles" that people laugh about, where the song is pretty much saying is that science is irrelevant since everything we're seeing is actually a miracle created by god and thus the "why" doesn't much matter. In the case of "Final Fantasy 7" this is literally true because the technology is being powered by energy vampired out of the divine force holding the planet together.
That said it's probably true that some of the games do have the message mentioned. I did not play the portable game mentioned, but it does seem like it could be a giant mind screw as well, the whole "video game character, confronted with the fact that he's a character in a video game" schtick.
Now, if you want to get into a game that has more of the message being talked about here, the series to look at would probably be "Shin Megami Tensei" in that one they even spell out what your doing in some titles. Of course it can also be argued that the divine forces in that game are portrayed as genuine, your just elevated by some means to eventually play at their level. I mean in some games like Nocturne the world pretty much ended. In the "Persona" spin off it seems to use a sort of logic similar to DC's "Sandman" where gods and such are very powerful, but the actual real powers are primordial universal forces like death which exist far beyond that level. Hence the whole "Memento Mori" thing in "Persona 3", basically when even gods can die your time as a very mortal being is of course going to be limited, no matter how powerful you become, and what you do in the course of the story (which gets pretty crazy) at the end death still takes you (even if he's kind of your friend).