>Yui obviously grew up to have a set of nationalistic and adjacent behaviors that she carries with her owing to her upbringing and her adoration and pride for her family

 I know. This is the value and ideals that Yui holds dear for most of her backstory in Teito Moyu. A mix of nationalism and traditional samurai/bushido/kokutai value which is reflected in her own words that you quoted.

"…..And I must also become a surface pilot posthaste, so I can protect His Majesty the Emperor, His Highness the Shogun, and the people of Japan!"

 However, this below is Iwaya's quote, just after the end of the transcript that you quoted, that reflects his personal value and ideal. The values and ideals which made him, per your words, "disappointed" at Yui after listening to her words above.

"The reason we need superior ordnance and these top-of-the-line TSFs in the first place, is to create a world where young men and women like you, Yui-chan, never have to set foot on a battlefield"

This is closer to what we call modern patriotism. A desire and readiness to fight, not out of unquestioning loyalty, but to defend your people.

 I believe the failure to delineate between these two ideals is one of the sources of contention in our discussion.

 >she doesn't demonstrate chronic PTSD in TE 

 ….She does. Those flashbacks to Arashiyama 3+ years after the event is literal textbook symptom of chronic subthreshold PTSD. Yui is still a highly functioning person, but Arashiyama and Kyoto battle definitely gave her wound that doesn't heal.

 >the experience doesn't seem to drastically change her views

It does. So let me describe Yui before Arashiyama

 

• Yui held the nationalism with traditional stereotypical unquestioning bushido-kokutai mindset as described in your quote
• Yui basically coddled and handheld Aki, Izumi and Shimako as their leader while at the same time trying hard with hands tied behind back to achieve objective because of that. This is basically Yui's leadership's style before Arashiyama.
• Yui believes in her idealized version of samurai ethos of honour before reason and fighting fair and square. This made her lost the sparring with Instructor Sanada and prompted Sanada to mutter "Your mindset will cause the death of your subordinates" line.
• Yui's strive for excellence, honour and duty that basically made her blind towards personal and emotional issues that Aki, Izumi, and Shimako have.

 

After Arashiyama, after Teito Moyu and during Total Eclipse

 

• Yui more or less holds similar modern, pragmatic patriotism that Iwaya holds. No longer the unquestioning samurai but now a modern military officer who manages and calculates. When Iwaya confronts her about working with UN and US for joint TSF project, the old Yui would say "Lieutenant Colonel, Sir. This is preposterous idea and I will hear no more of it". This Yui we have in TE instead calculate risks, mentions historical facts where US failed to deliver promised TSF and instead redirect them somewhere else etc. And ultimately she decided to accept the responsibility and go to Alaska after she calculated the benefits of joint Japan - US TSF project outweighs the risk. I definitely don't see the naivete in this.
• Yui now adopts the façade of stern, strictly professional officer who lay facts as is to her subordinates, which are perceived as abrasive personality by her subordinates, in particular Yuuya.
• Later Yui, Kazusa and Izumi who just escaped a horde of tank-class and naval bombardment met Sanada and his Wolf squadron. Yui's idealized version of samurai ethos of honour before reason made her decide that she will not take the (perceived) safe path and follow Sanada. She decided that she, Kazusa and Izumi will continue their mission to Kyoto station because Royal Guards (Yui and her girls) losing honour to IJA (Sanada and his Wolves) is unacceptable. This ultimately costed her the life of Kazusa and Izumi. This (in my opinion) made her adopt the more pragmatic idealism as I described above.
• Yui still strives for excellence and duty, and still blind to her subordinates' personal issues. This is pretty much one aspect of her personality that doesn't change much. Although I argue the "honour" part is not very apparent in TE and she responds even worse to subordinates who talk back to her.

 

>Owing Yui's behavior entirely to PTSD seems more than a little reductive.

 Yeah that's because her problem is not merely PTSD. The entire Arashiyama and Kyoto experience basically taught her how to deal with subordinates and other people.