At least in my games I play them like this.
Every sector, and in some cases subsectors or even specific forgeworlds, have their own traditions and rules. Therefore, each one has their own different kind of Skitarii.
Actually, with very few exceptions to rules that encompass the full Imperium, I do this for most aspects of the setting.
It's a good approach to take - why do you think the 40kRPs always have their own sectors? A corner of space unique to each RPG, allowing FFG to detail things without having to make sweeping declarations about the whole setting (which, amongst other things, speeds up approvals - defining something as specific to the RPG 'sandbox' means that GW is much more likely to give it the thumbs up.
That's what I love about WH40K against, say, Star Wars.
Ironically, although the Imperium is a massive, monolithic, overbearing government, WH40K is not a massive, monolithic, overbearing setting.
Each sector, subsector and planet has their own culture, it's like the game has multiple different settings with some constant points linking them.
Although many fans of the settings dislike Abnett's books, I love them because of this. They show the width of the Imperium, it's many cultures, even in just one small part of the Imperium.