First, the "Can't fit round pegs into square holes" is a reference to Roget's proposal for SCP-001. Apparently by using some Keter SCPs / releasing them it's possible to change aspects of reality. A VK-class reality restructuring as they call it.
Second: There is a hidden text in the blank iteration. It reads as follows:
And it is in the humble opinion of this narrator that strange things happen all the time. And so it goes, and so it goes. And the book says, "We may be through with the past, but the past ain't through with us."
Thirdly: Here's a long post from the author explaining a lot of his ideas in this article:
Glad you liked what you did, sorry you didn't like what you didn't. I'll acknowledge it's not perfect, but it was a pretty ambitious thingamajig. The idea behind the "make idea not you, forget idea you" is a threat from the sort of beings that the Lox represent: in the same way light has dual particle/wave properties, the Lox have dual corporeal/memetic properties. They can exist as physical bodies or as thought patterns or ideas. Such beings would have concepts of death applicable both to corporeal beings and memetic concepts; what the infected individual is trying to say with the "make idea not you, make forget you" is "We will make you forgotten", i.e. "we will destroy your idea". It's a valid threat in their society.
Yyyyeah, sorry about the length. It's an attempt to replicate the bureaucracy that would be involved in the end of the world, so convenience would not necessarily be a factor. The first three iterations are near-copycats of one another because I figured that was what the Foundation would do — only update the relevant information. I couldn't think of a more effective way to isolate only that.
Our viewing of Ruhar formed some sort of connection that allowed the idea component of Ruhar to enter us. (That sounds really stupid when phrased like that, but I think you get the idea.) Adidal didn't actually know about humans before this point and wasn't aware of that characteristic; it's unique to humans as a species, so far as Adidal would know. The universal nature of the broadcast and the lack of specific aim at humans is supposed to imply the presence of many other intelligent species that Adidal is expecting to receive the message. The motivation is to intimidate those other species — any receiving the message, really — into understanding "We, and myself (Adidal) in particular, are not to be fucked with. These are the consequences."
I have no idea what the next two sections ("Pages leave into past" and "Paradox create you?") mean.
The very short time span of the descent of humanity into theocracy and cannibalism, not to mention the near complete abandonment of even cursory attempts to fight the aliens and the determination of humans just to slaughter other humans because we're frankly just better at that, was very deliberate. Hopelessness.
Adidal almost certainly could have communicated with humans very directly and clearly; it's just not his style, per se. The Lox are his hounddogs, his enforcers, and their ability to communicate in our language is likely rather flawed. I would presume that had we captured a Drone that had been containing a Lox in him/her for a longer period of time, they would have a much better command of English due to a greater familiarity with our speech centers and vocal apparati.
That should make reading 2998 a lot more fun, and should keep people who don't know many SCPs busy for a long time with all the cross-referencing…