If Chapter 1 of the Lost Logia Incident Report was the first exploration of ship-to-ship combat between the Halo universe and the Nanoha one, Chapter 2 (appropriately named "Boarding Action") deals with personal combat.
The Bureau Marines are the first to respond to the attempted boarding action, and they're hopelessly outclassed. In shipboard corridors with minimal cover against foes with sufficiently powerful weapons, equipped with armor that was most likely designed to defend against magical attacks? And now that the Bureau is reduced to more "conventional" attacks, rather than the ridiculously overpowered Arc-en-Ciel, the Elites' defensive shielding comes into play. All of this combined to create an off-screen battle in which the Bureau Marines got massacred. (Of course, even without the tech balance, it would hardly do to have the problem dealt with before the main characters arrived...)
Chrono, Nanoha, and Fate, however, are an entirely different story. They're significantly more powerful magic-users with both defensive and offensive magic. Truly, this is where the Bureau's advantages matter most: in individual combat where each of the Bureau mages can fight in their own preferred styles. As I see it, Nanoha, Chrono, or Fate are all individually at least the equal of an Elite, with defenses that are at least as powerful and weapons that are usually more effective.
They do have their disadvantages, but in this situation against a limited number of Covenant foes, those disadvantages don't really come into play. Most noticeably, Nanoha herself ends up using her stun setting to attack. In the first two seasons of the anime, her only battles were against clearly inhuman monsters or against single foes in situations where a KO would be just as effective as a kill. For now it doesn't seem to matter; the Elite that she targets is just as out of the fight... but not all of their fights will be as accommodating.
Once the boarding action is cleansed, I took a step back to summarize. The Arthra has severe damage (precisely because the Arc-en-Ciel was so incredibly powerful, it was first on the list of things to disable), but the presence of dimensional rifts and the clearly unnatural ring world override those concerns, and Chrono, Nanoha, and Fate are thrown back into battle. This is another point on which I worry that the decisions made were unrealistic - perhaps Lindy really would have retreated. Of course, if I want the story to continue, I'm not left with much choice. And so the Bureau doubles down, sending its enforcer and two assistants down to the surface of Halo.