I understand what you're doing (fleshing out things in the story) and I'd have to play the game to find out more. However, the first underlined scenario doesn't really sound like a plot hole; more of a "if-then" scenario.I did answer this question before, so I will summarize. Basically in the VN, humans are little sheep, they can't fight monsters at all, also it's hard to take a grip in what is monster girl society (someone must keep the monster lord castle working, and that require money and manpower). One example which I will fix here in this version 0.2 is Granberia attacking San Ilia Castle with ease. If she can do that, there is no way a war can exist, because if she destroy that place and kill the Pope, she would make the humans disorganize, destroy their economy and their way to fight back. If you destroy their way to fight back, nothing stop the monster girls to enslave all mankind putting an end to the semen shortage, pollution, etc. Each monster girl could have 2, 3 slaves, and there is no reason for Alice don't allow that to happen, it is in the best interest of the monster girls which she vowed to protect.
There are other minor things like Luka defeating a Queen alone when he barely began his quest, Alma Elma attacking a ship and no one lifting a finger to stop her (it's a ship in the middle of the sea, Did they think they could run away?).
There is many explanations missing in the VN as well which I will try to fulfill here.
I also am changing somethings which aren't plotholes, but that in my opinion it's better the way I'm making, as well some additions, quests etc.. I'd suggest you play to see what I mean, but I do suggest you wait a few more days before trying, since I will launch the version 0.2 soon, it's already being tested and will go until Sylph.
The second underlined section actually was pretty well explained in Chapter 1. I don't know how to tag spoilers, so I can't go into it.
A couple of legit early plot holes are 1) why did Ilias never show for Luka's baptism or 2) Why did Alice just happen to be carrying around Angel Halo, a sword Luka could wield to use against monsters. Both were fully explained by Part 3.