Kaphotics

That's the default behavior. Questions about how sysbots work is irrelevant to this thread.

Per the program's readme, you need to dump the full game as well as all patches into the romfs. Having unpatched (1.0) data will fail to be recognized.

You've only played 42 seconds. Properly save in game after receiving your starter.

dst are save states; save in game to properly get save files "bak" files are backup... the program is likely overwriting the dst as you told it to, but it additionally creates a backup since you overwrote the original.

Thanks, will be fixed in future releases. If you have the automatic backup setting enabled, you don't have to manually create them. Don't overwrite existing backups with that button, hence the (current) error

The move shop button is right there. Give it a try. Hint: form argument tracks usage.

Load a proper save file

Without knowing what moves you gave it, can't know for sure. Ensure that PKHeX said it is legal. Starting in P:LA, the game bad-eggs anything with a move it cannot learn.

PKHeX does not support ROM hacks. I force-loaded the save file, and the pokedex says you started with a Murkrow and have captured nothing else, and the boxes haven't been accessed in your 18 minutes of playtime. If the ROM Hack has modified how the save file is stored, then PKHeX will not be able to recognize it even after you've access the storage boxes in-game.

Save data is corrupted; PKHeX is correctly rejecting the data as it is completely malformed. Extract it correctly and transfer it without damaging the save data. Assuming it is still playable, you are likely not exporting/transferring it correctly. Transferring via FTP with incorrect settings (binary is correct, not ascii text), etc.

Save correctly in-game, and use a more recent save file editor like PKHeX.

Per the stickied threads, PKHeX requires net46, which is newer than net40. Keep in mind that customized forks for ROM hacks should be inquired with the fork author, as their modifications are not my purview.

Unable to access file 'Z:\usr\src\packages\BUILD\dlls\msvcrt\wcs.c' I'd start there. I do not know how to resolve that.

Nothing in that dump looks to be indicative of PKHeX code at fault. More than likely it's your OS/wine install having a bug outside of PKHeX's control.