sora10pls

They're not incompatible, but rather, PKHeX is expecting a file format extension that PKHeX generates when loading files into the database. RoC's PC contains .pkm files for a lot of the older games, which is the extension PokeGen uses for all of its Pokémon entity files, regardless of the generation.

Reported and fixed weeks ago already. Use the dev build or wait for the next stable release.

You can dump AHTB with pkNX and load it locally next to PKHeX.exe, then set all of the FSYS_FLY_<loc> flags.

PKHeX does not support ROM hacks. Please do not upload ROM data here, as it goes against the forum rules.

If you're playing on emulator, you should have a hacked Switch in order to have dumped your games to play on emulator. Piracy is not supported here.

Download Pokémon HOME and move them up to Scarlet/Violet through that (does not require a premium subscription to do this). Parasect is not available in SV, and Tentacruel was not available in SV until Ver. 3.0.0.

You should try again with a real save file obtained from a Gen3 cart, not some shady website that lets you play pirated content...

As you fill up your dex in SV, the game will endlessly nag you with notifications saying that there are rewards you can claim for reaching certain milestones. Go to your Pokédexes in-game and evaluate them to reach all the milestones to claim the rewards. Notifications will go away after that. Not a PKHeX bug, that's just how the games work.

Like I said, it's working fine. You're reporting Pokémon that were generated with the initial Indigo Disk support release of PKHeX, which assigned 0 Weight/Scale to all trades. This has since been fixed, even before you reported the issue. PKHeX is flagging them correctly. Per the first post on this thread: NOT FOR USER MISTAKES OR TROUBLESHOOTING HELP.

Works fine.

PKHeX released: October 11 2023 Typhlosion released: November 3 2023 PKHeX can not know of future releases. Either use the latest development build, or wait for the next release.

Unable to replicate

Not a weird behaviour; PKHeX hides any species that are unavailable in your current save file (yes, this includes blank save files). Ivysaur, Squirtle, Caterpie, Pidgeotto, Nidoran♀, Nidoran♂, and Abra are not available in SV, so displaying them in the pkmdb would be pointless because viewing the resulting pkm and trying to convert it to a PK9 would always yield an illegal result. The setting you noted is simply there to help display everything regardless of availability, which is what you want.

Working as intended. Fog is not available as a weather condition in Wild Area until post-game, where all of your encounters would be boosted to Lv. 60.

That is not your save data, that is extra data. Read the guide if you don't know what you're doing.