The muddying of the timeline is just a continuation of a policy GW has been pursuing for awhile similar to when they removed dating refs from the fluff in recent codexes. Does it matter? Not really, unless you are of the type that likes to know exactly when something like the Badab War happened.
One of the keys to 40K is that being "the type to know exactly" doesn't really work out well, because you can't know exactly. Even with the "date stamps", all you truly knew was the approximate refencial time frame in which the event was recorded as happening. You could say "Badad War started about 55 years before blank, and went on for 10 years", but to say that those dates were perfectly accurate has always been somewhat of a misstatement for a setting where not knowing something perfectly is more likely than knowing it perfectly.
People act like all the mechanisms of society in the Imperium are as exact as our current world's are (and if you are truly honest, even ours aren't that
exact). We have a "single history" and "acknowledged historical timeline" because it's important to some folks on earth to establish those things, and since there's factual data, a lot of people not involved in any way become accepting of it. That doesn't inherently mean it's perfect though, there are people that disagree about the facts, have alternate views they present as facts, or disagree with the data and say it actually shows something else. That's just one planet, with a population capable technologically of having those kinds of discussions.
Now imagine that you have multiple planets that may or may not be capable of that, but don't have instant communication with each other. You can imagine that things might begin to get misaligned between them. Toss in the capabilities of an organization that not only can alter the history books (one of Earth's big benefits), but has the capability to convince people that they have misremembered or outright alter memories (or completely take them away, leaving you to rely 100% on the revised version).
It doesn't make for a situation where anyone can actually accurately know with atomic clock precision all time-date stamps on every event that occur, especially when information is given at best from the view of a semi-omniscient narrator. The need to do that seems more like an exercise in frustration for discussion and counter to the knowledge presented for the setting.