>>23312059https://www.youtube.com/watch?v=4bqivMilCTkI helped discovering this, along with
>>23316818The removed texts probably point to a previous different plot that was probably in the game. Silph's Chief (a scrapped trainer class, also) was originally evil and in this instance he was hiding in the Safari Zone, here's why there is "machinery" in the Secret House. Maybe the player could bring its own Pokémon in there, this is also suggested by the fact that there are Pokémon Center signs in the tileset data of the Rest Houses.
Probably Silph's Chief worked alongside Giovanni, who had a different role and might have not even been a Gym Leader, since his name is not on the Gym Leaders list in the RBY text dump, instead Bruno is the first in the list, so originally Bruno was intended to be the first Gym Leader, perhaps.
Also, pic related. It can't be seen normally in game, but only with a walk-through-walls code.