Regarding the Valkyrie Profile 2: Silmeria, the present config is not working properly, as I wrote in the wiki. I have made a proper port of the Maori-Jigglypuff's rebuilded code using the 0x42 overlay command. The result is the protection is ignored indeed. But there are some lines left to patch, related to the protection traps (0x00100A7C, 0x00100BB4, 0x00100C64, 0x00143614, 0x0014533C)
and the audio/video synchronization (0x0010D138) (probably not needed in the netemu due to the asynchronous mixing of sound). The problem is the netemu has got some troubles to patch them properly, because the protection is triggered somehow. I tried to patch them statically, using the 0x0B command. And the outcome is very bizarre - the values in the 0010xxxx range are left unpatched completely! Patching them using the 0x0A command makes the game to freeze after the first battle.
Could the 0x01 hooks interfere with the patching or the protection? The first, 0x0A, hooks the address 0x00100928 (so it's near to the ones we want to patch). The second one, 0x0B, is present only in the GX configs and hooks the address 0x002B9808. I know the first one is related to the ELF unpacking, I do not know what the 0x0B hook is responsible for.
Looks like the Japanese SOFT config of the Valkyrie Profile 2 does contain a partial protection patch, since they were rearranging some code by the 0x0B command. But their 0x0A hook address is different.