Mankey and Bulbasaur do not exist in Legends Arceus, so you can not convert them. Same with Onix which does not exist in Scarlet.
Mankey exists in Brilliant Diamond, so that one works.
Starting with Gen 8 GameFreak decided to cut some Pokemon out of the games. They don't even have data/models for those. Some Pokemon might get added through DLCs while others will remain unavailable.
Well, it's exactly like that. There's only PID, Moves, Species, HeldItem, Level and EVs (not per stat, only one value that's applied to each stat).
PKHeX already has the data structure, it's just missing a GUI.
Start a new save and import the Gen 5 Living Dex pcdata.bin from here. It has all Pokemon but on different levels.
Alternatively you could use the ALM plugin and generate your own Living Dex mons. All will be level 100.
https://github.com/santacrab2/PKHeX-Plugins/releases/latest
The latest version of the plugin (2.2.2) should work fine on the latest version of PKHeX (24.03.26).
The plugins folder has to be next to the PKHeX.exe, so like this:
The plugin also won't show up if you don't have a save loaded.
The file is full of garbage, no real save data inside.
Besides that the proper size for Gen 3 saves is 128kb. You should check if FlashGBX is able to dump the full 128kb save.