Tbh unless Van invents the proximity fuse, hitting a flying target with ranged weapons is quite hard. Even then, the wyvern riders would eventually learn to fly low before striking, so that the trees and terrain block the ballistas' firing angle, mirroring SEAD tactics from our world.
Even with Esparda and Van casting shields, the riders can still attack from different angles simultaneously, making the shield moot unless it can cover the entire anti-wyvern formation. Best Van can do is prepare emplacements with overhead protection, at the cost of firing angles.
You make great points my friend......now here's my major counter
All you said COULD happen if the Empire doesn't just dismiss the bombs and bombing run idea as "pointless" since "it failed!"
That's kind of the risk that happens when something FAILS on it's "maiden voyage/Test Run" Since the Empire lost pretty HEAVILY here. The idea might survive and what you said could be implemented ONLY if they give it another chance and use your idea, which might be scrapped, and if Wyverns and/or Puppet Mages are not so uncommon! The risk might not be made (if however that strategy was used AND showed results which as you pointed out it would! THEN it would be considered, but that would have to happen by mere ACCIDENT as these things usually do LOL)
Odds are as said, the Empire which will be too busy licking their wounds by the EPIC FAIL of this operation that had to take years, resources and ALOT of patience moving everything around without the Kingdom noticing (as the King said the chapter before when they learned of the invasion, they thought they kept a good eye on the Empire for this, only turns out the Empire lulled them into THINKING they weren't preparing for something!
In a WHAT IF (Van is killed by his father), it's very clear things WOULD have gone their way here! Van's dad dies here (good karma even IF he is a "Father to his men", he still sucks for how he treated his sons, though that's the dark side of the mindset of those who take "Meritocracy TOO SERIOUSLY" especially if you get an idea of WHAT THEY VIEW AS MERIT which as he made clear before this invasion, he didn't think much of Van, only giving him as he saw, "credit for having good memory, but that was it!" And as you learned with why EVERYONE ELSE including his former Butler were willing to follow him! It's likely in his mind, Van didn't MERIT anything because had he gained the ELEMENTS, most specifically HIS element of Fire! Then maybe he'd have changed his mind, but he ended up with Production Magic, a Magic viewed as USELESS for what my counterpoint illustrated, once failure was seen and continued to be seen with Production Mages, the entire Magic was deemed POINTLESS AND USELESS! No studies, NOTHING. It's considered DUD MAGIC! But for Van "who has good memory and past life knowledge of the modern world" his "Experimenting" allowed him to effectively turn it into a VERY OP Logistics Power! I say that cause this isn't a power for FIGHTING which is limited by how you set it up, and by FIGHTING, I mean "direct fighting" like how the Element magics are used! I mean look how Van helped Aria utilize her Puppet Magic, create a huge golem doll that she can pretty much use as a "Medieval Mecha!" This could revolutionize Puppet Mage's in combat situations! They essentially have themselves MECH PILOTS if they could repicate the Giant Dolls which I believe could be made even WITHOUT Van's Production Magic LOL) and they take over the region. They continue to utilize the same tactic, if not EVOLVE IT to avoid countermeasures being made. That explains abit more on the LOGICAL SIDE of "attacking the fleeing civilians!" The LESS knowledge of HOW they took the fortress and region gets back to the Kingdom, the better for them! Guess the Ethical backlash later was considered ACCEPTABLE if it leads to them conquering the Kingdom BEFORE a countermeasure could be formed!