Actually, Sims started out having to be hacked and forced to load files. It did not want to, and there was a framework installed that specifically told it to use recursive directories to load mods from. It wasn't until later that EA built it into the game. Surprising, I know, that they did this. The only reason it was even possible in the first place is it loaded a config file that allowed you to define paths for package files (likely part because it's a PC game and who knows where they might be in a given build, considering their unique expansion pack design)
They even made the game check for core mods made for other versions instead of going "Waaaagh" and puke all over itself. I never expected it from EA of all companies, but there it is.
SR4 unfortunately assumes files are loaded from a flat set, and the engine runs accordingly, even inside the vpp_pc files they're still flat compressed. The closest we have is the str2_pc files which contain other files, but are loaded all as a single streaming set. Changing that would probably come to rewriting the engine entirely. It is made for consoles remember where it's all one disk to load from. As noted, the closest you're gonna get is packing them into patch files.
Besides, just do a search for xtbl, lua, str2_pc, and asm_pc files. Any of those from Volition are packed into the vpp_pc files in the normal packfiles\pc\cache directory, so any in the SR4 (or SR3) root are mods.