As a player of a good year and a half(soon to be DM?) here are some of my thoughts on a few of these points.
The article regarding Monstrous Races(3.1.g) suggests outright telling people how they're allowed to RP their character, in the bad way. I feel this connects closely with the point brought up in 3.1.b, so long as the nature of the character does not undermine the rest of the table it should be fine.
Regarding races that have flight, Article 3.1.e, I'm not sure what the problem truly is. If it's the idea of the player being able to fly off wherever they please... well, I'm of the opinion a DM should then be able to go "Okay, can you pull out a character that will be playing the game then?" But of course, Fly and a variety of magic items allows the same "issue" to happen. If it's about combat, a flying player is the biggest target for ranged attacks and there is a deadly risk of having Hold Person or some other incapacitation to hit you and send you spiraling to your death.
When it comes to PvP, from Article 3.1.b, I too agree it has nothing to do with alignment. But I'm also of the opinion that both players agreeing to it above the table is a good way to keep things fair. We have no system in place to label games as "PvP Allowed" after all, and some may not be looking for an experience where their character can be put in harms way by another player so easily without knowing about it.
Magical Items. Article 10. I've never been a fan of this one myself, and it especially hurts higher level games where a simple potion of healing is, to be quite honest, not even a drop in the bucket. There's also something of an issue of no one having anything to do with their gold in the MV. I think a better system would be to restrict what types of items can be sold for different tiers of levels. Players in the 1-5 level range should possibly get access to Uncommon items for instance... but not Very Rare.
For my own part I'm actually in favor of implementing some kind of Tagging System so people know what they are getting into. In AL you don't really get the benefit of a Session 0 to know what you're going to play, and that is currently the case in MV but I think we can do better. Simple tags such as [High Fantasy], [PvP Allowed], [Deadly], [Heroic], [Open World] and so on. This would be something listed next to/under/above a game and which tags are used would be 100% DM discretion.