Well, after a while she cool her head and realize that she was wrong by saying that to leon (even though without her knowing that she told the truth to leon) she tried to apologize but the sky pirates are attacking at the moment but she keep trying yo talk with leon some robots are there to stop her but her power stunt them and she reach partner's deck at that moment the sky pirate's leader appers and try to capture livia bu Brad and Greg protect her, Leon Saw this and Snap thanks to his fight with livia he was already thinking because he is a mob he should be close to Livia watching brand and greg saving livia feel so natural for them to do and leon Said that he is a mob and he was never ment to be with Livia becoming more merciless with arroganz, brad and Greg are defeated and livia try to run but the pirate's leader threat her with killing brad and greg at that moment Arroganz's Hit Launch him out of the way at that moment Livia is Happy and Glad to See arroganz but soon she feel Fear by watching Arroganz, by her PoV Arroganz was this Cute and funny armor but Now It looks Evil and Merciless this is a Reflection of Leon's Mentality at the moment, he feel frustrated by the sight of Livia and the two idiots ( he had yet to realize his feelings for Livia) at the end of the Fight, Leon called her Olivia and she start to cry feeling the Gap in the Relationship got Bigger. Later angie Shows up and Slap Leon for making Cry Livia but she is in the same situation with her relationship with livia so she can't said nothing aginst Leon. This will continue until the Ambush of the Principality at the school trip where Livia Tell leon that it has to be Him Not other Guys this destroy Any escape for Leon using the Excuse of the Game's plot, he accepts that his actions already destroyed the Game's plot and refuse to Leave Livia in the hand of the Useless five.
Even if His protection was the correct Action ( and after Reading what would happened to Livia if Marie Didn't get involved and she gets Leon's protection, we as readers Knows it was the correct choice but for them it would be unknow what happened in marie's route) but even if i was the right choice Livia's words points out a fatal flaw in leon's character , his Overprotection and how out of touch he is with the reality around him, his overprotection is the reason why marie was such spoiled brat in their previous life he didn't allow her to face the fallout of her actions until he died and by that marie had to suffer a lot after that and looking how he never look livia, angie or the five idiots as a persons but as fictional characters bound to a plot, he even belived that his actions wouldn't affect the plot if you see he keep saying this world is that Otome game he refuse to view the world as a reality until he is in danger until livia points out how he treat her as pet this mentality of leon start to shatter and is finally broken at he end of the arc.
in Marie's route Leons accept the world as Real and start to get involved with it stopping the final bosses ahead of time, this allow to discover the plot of the principality and saving both princess (only one survive in the main series) also Leon Recover one of the Artifacts of the Saint and marie's used discovering that the artifact is haunted by the vengenful spirit of the saint that try to take over her descendants bodies (Livia and Marie are her descendants) thanks to marie Strong Mentality she can't be possessed but Livia in the other hand is suffering a lot (she even had mental breakdowns when she is alone saying "it will be fine, it will be fine, it will be fine, it will be fine" that was hard and sad to read after 3 volumes building her character) and got possessed when she found the artifact in the dungeon and now the saint use her body to destroy the kingdom.
With Luxion let's remember he is a AI even if he can show some emotions he still ruled by logic and results, he only said that leons protection was bad in the long run because Livia lacked of "spiritual Growth" but later he points out that thanks Leon protection she was able to focus in her studies and became better at magic when she use powers that in the game would need the Saint's artifacts to use it (also he have no way to know anything of what happened in other timeline so he can only criticize leon by the result he had witness)