Well the NG+ does fix a lot of issues since Towerfag actively updates that section. A fresh new game has a lot of old issues since certain parts of the game have fallen under neglect over the years, such as the Kobolds arrays not being defined correctly. Various things could be improved by making sure arrays are properly initialized, it sometimes happens with all the randomly generated NPCs...
There was an save bloat thing that I don't think was every really fixed. This happens when a save file gets significantly larger than 20 MB, I speculated it might have something to do with the Path Finding however every save I looked at with this glitch would shrink and that was probably do to the debugger I attached... Since Auto Save happens at end of day if I remember right (It's been awhile since I've dived deep into things) that that could compound the saving/loading problems.
Then again I discovered some problems with how the scripts were placed in Common Events. An example off the top of my head is the Cardinal Bell and how it changes genders, somewhere around when you select a character and it waits to execute the command the NPC ID gets changed by something else which results in the wrong character getting altered. Probably not an isolated occurrence but some of these Common Events have a firing order that's like a train engine...
The Achievement System is also capable of slowing things down substantially so if you haven't tried cheating it might be worth it for the performance boost
The patch you noticed only forces the populations not to drop so something could be unique with the Bird Realm.
If you wanted to could try decrypting the game and using the Script
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and see if this problem persist.
Depends on the patches you're talking about but most of mine override the Common Event they are associated with. While it takes more time I tend to keep them separated by the functions they do and most of what they do are explained in the notes.
The official patches tend to handle various bugs though the bug in the that handles Maps was never officially addressed.
As for modding this game having RPG Maker VX Ace Editor,
RGSS-Decryptor, and some knowledge of Ruby would be helpful. Just make the changes you want in the Editor, use the Patch System to save those changes, and distribute the Patch that is generated. Should be noted that the Patches take a naming precedence and if you haven't used the unofficial fix provided by Happily_Hitsuji only the last patch with Map Updates will be the one that is used, this doesn't effect Common Events though the last one loaded will still be the one to alter that specific Common Event.
Edit: Almost forgot a very important thing, for the love of cheesecake back up "System\RGSS301.dll"! This game uses a custom dll and if you don't use that specific one the resolution will get jacked when RPG Maker VX Ace Editor overwrites that with a generic one.