1. I am a Trooper Commando, playing False Emperor flashpoint in Story Mode, with a companion and Combat Support Droid. Just before my trooper’s final fight with Malgus, Malgus sends all his guards away, consisting of more than a dozen men with lightsabers and attack rifles.. Why did he send them away? They were numerous enough to defeat me if they attacked me all at once. It seems unlikely that Malgus was concerned about making this a “fair” fight. It also seems unlikely that he felt confident enough to take me on alone, after I’d reached his throne room after fighting my way completely through that incredible and well-defended space station. Why didn’t he order his guards to attack, instead of removing them from the fight?

2. Just before the fight with Malgus, a female voice announces that the station is about to explode. Is Malgus surprised that this is happening, or did he set it in motion himself? He says, “Arkis Wode, well played”. Does this mean that he was surprised that Arkis Wode changed sides, and he thus realized that all was lost?

1. I am a Trooper Commando, playing False Emperor flashpoint in Story Mode, with a companion and Combat Support Droid. Just before my trooper’s final fight with Malgus, Malgus sends all his guards away, consisting of more than a dozen men with lightsabers and attack rifles.. Why did he send them away? They were numerous enough to defeat me if they attacked me all at once. It seems unlikely that Malgus was concerned about making this a “fair” fight. It also seems unlikely that he felt confident enough to take me on alone, after I’d reached his throne room after fighting my way completely through that incredible and well-defended space station. Why didn’t he order his guards to attack, instead of removing them from the fight?

 

2. Just before the fight with Malgus, a female voice announces that the station is about to explode. Is Malgus surprised that this is happening, or did he set it in motion himself? He says, “Arkis Wode, well played”. Does this mean that he was surprised that Arkis Wode changed sides, and he thus realized that all was lost?

These questions both have the same answer.

Malgus respects two related things that are sometimes in tension: strength and cunning. He understands the limitations of sheer brute rage and xenophobia, hence his (Imp side Ilum) struggle with Grand Moff Regus and (both sides) the partly-nonhuman foundation of his New Imperial fighting forces. But he also is still Sith, and he still couches his arguments in terms of strength. His New Empire is for the strong, regardless of race or background. He wants the opposing forces to show him their strength. So he is impressed by strength and decisions that show strength of some kind, especially if that strength is intelligently applied. Hence the Arkis Wode comment; he recognizes the strength of a light-sided decision there and approves of it, because he is both about force and the intelligent application thereof.

And as for the throne room, sometimes Malgus himself demonstrates his strength by using his followers, and other times he wants to show it off himself. It's not necessarily about fairness. After all, he does send a boss rush at the player(s) over the course of both flashpoints. It's probably more about exercising personal strength, finally getting to enjoy a proper fight, that sort of thing. One suspects that fighting the player(s) in tandem with a bunch of Imperial Guard would be less interesting to him than the alternative.

There are some other parts of the game that might be regarded as spoilers that would support this analysis.

There's also a fairly prosaic and non-lore-related answer for your first question. The False Emperor, as the end of the vanilla story's content, was meant to be a sort of Return of the Jedi moment for every class, from the space battle raging outside to the struggle inside an Emperor's throne room. So, just as Palpatine sends away his Redrobes ("Leave us."), Malgus sends away his New Imperial Guard for a more personal confrontation.