As I understand it way back in the early Beta days of Minecraft obfuscation was added to avoid mods being embedded into the JAR and it being released as a combination enabling piracy of the game with mods embedded.
This has been a pain to workaround for years as the modding scene has gotten bigger. Hopefully this makes modding a bit more accessible.
The later generation mod loader use preloader and asm hooks though. So the file isn't even physically patched, just patched in memory. That is such an old day that you still need to patch the jar by yourself. (If I am not remembered it incorrectly, I think the community change happens between 1.3 and 1.5?)
Yeah I still remember when you had to manually patch your minecraft.jar with mods. Always remove the META-INF directory so it works. Back then, when you installed two mods that were incompatible with each other, you had to throw away the whole minecraft.jar and start again.
This already changed A LOT when Forge and later Fabric came out, with a simple patch system akin to BepinEx and a mods folder.