Routes 47 and 48 are now canon routes.
Route 47 and 48 exist specifically in HG/SS which is an alternate continuity from Gold and Silver on Gameboy Color. The continuity from the Pokemon games that Brown and Prism borrow from is solely based on the original games, not the remakes or re-releases (such as Yellow or Crystal). Therefore Route 47 / 48 can exist as different routes in Brown/Prism and HG/SS.
Pokemon like Larvitars might be too tough for Merson Cave, but I see your point. I'm not going to add mini games to Brown, it's just going to be improvements to the game design flaws.