I'm not sure where you're looking but I just checked and the Complete softmod guide and wii guide both instruct you to use the d2x cIOSs. If any guide you find is using something different it's outdated or inferior. If you're referring to d2x v8 final versus v10 beta 52 or 53 the differences are minor, in fact beta 52 is the same as v8 final, and beta 53 trades off compatibility in order to use both USB ports for USB loading. V8 final is optimal, but if you want to install beta cios's you can instruct modmii to do so by typing "beta" on modmii classic's download page 4 and selecting a different version of d2x cios. ModMii was the original d2x cios installer (in fact the X in d2x stands for XFlak), so it should be no surprise that it can build beta releases hosted on the d2x repository.
A patched system menu IOS has a few advantages and the wii community generally agrees its the way to go (nothing I did with ModMii was dictated, but rather I incorporated widely believed best practices into ModMii). One such advantage to installing a patched IOS60 into all SM slots is extra brick protection. This will protect against downgrade bricks in newer LU64+ consoles, or 003 bricks when region changed originally Korean wii's are upgraded. Most people don't know whether their console falls under these categorizes, so using the system menu IOSs supplied by ModMii could be protecting consoles that otherwise would've bricked and you wouldn't even know it.