"The Grass-type Pokémon", "The Fire-type Pokémon", and "The Water-type Pokémon" are all flavor text when choosing the starters; this does not reflect their actual Types and pk3DS does not update this.
pk3DS already warns users about this. If the user decides to ignore the warning, it's their fault, not the program's.
No, pk3DS does not force Legendary/Mythical Pokémon if those checkboxes are checked, it simply adds them to the possible randomized species.
Dump your game's update data using GodMode9, decrypt/extract it, and overwrite your existing ROM dump with the extracted contents of your update data dump.