I'd have to agree there. It's pretty much already been done anyhow in games like BFG where you had the optional campaign rules that covered things like repair and retrofit, resupply, reinforcements etc. not to mention Mordheim and Necro where the after battle sequence is just that, worrying about logistics. it has its place and can even be done in 40k but should be along the lines of BFG in that its an optional campaign thing.
But to address the OP's original question-
I have no problem with the fluff not syncing to gameplay. I am a diehard fluff monkey. I love reading all the little tidbits in the codices and the BL stuff, (Abnett and Mitchelson are my favs.). And all the changes you see from book to book i kinda look at in an archaeological sense. After all the Imperium itself is 40K + years old, not to mention any of the older races who predate humans. that's a lot of history to get right.
(i'm gunna go there) Look, fluff wise what it comes down to is this. In our world we have less than 10K years of recorded human history, and I'm just talking about when we as humans started writing stuff down, not what we know now of pre-record keeping societies. We are still discovering new and interesting things (artifacts and knowledge) that change our perception of previous cultures, and we are only dealing with 1 planet! put next to the Galaxy spanning Imperium and the ancient races that exist there, that's nothing.
I remember two stories, One was a short story and the other was a sidebar in some codex or other, that dealt with tech adepts that were basically the Livingstons and Indiana Jones of 40K. they both explored deep into long abandoned crypto-vaults and other repositories of knowledge to find forgotten tech and such. they were interesting stories that kinda shone a little light on the Historians and archaeologists of 40k who otherwise are unknown in the game itself. the fluff changing (in my deluded brain anyhow) just represents the findings of these types that become re-integrated into what is known by the common folk. Hence the reason older codices might disagree with one another.
Now having said that, Does the Fluff match the gameplay? not really! I don't believe it ever could really. When you read these stories you see things like this Orc Warboss can beat up anything, that Eldar is so damn agile he makes 14 year gymnasts look fat and clumsy, or all it takes to defeat a Dark Eldar raid is one under equipped marine. Essentially, what you're reading is akin to the Myth and Legends of lore that we take as granted in our world. It's Beowulf and Arthur or the Norse gods or Greek gods. The fluff (to me anyhow) represents the legendary actions and mythical prowess of the heroes of whatever armies' book you happen to be reading at the time vs. the "reality" of what that army and its' heroes can actually do in the(ir) "real" world. and then you add in the cost, (both physical and financial) of trying to represent some of the large horde/swarm like battles, sheesh, thats best left to apoc really, lol.
Some of the best fluff i've read didn't deal with those massive battles directly. they were about a single person, squad, company or even a regiment and how they affected their part in the battle. Even the regimental stories tend to focus on only a few key characters and show the units they control as a vague presence. so basically what I think I'm trying to say here is this-
The fluff is history and legend that is subject to new discovery, while the actual game play is the "reality" of the make believe world that we enjoy visiting. Make sense?