I know that there's a way to do this manually using SSH, but it's a huge pain in the ass to do it every single time I update the phone.
Has there ever been any talk about having PwnageTool alter system sounds in the ipsw file instead of just the boot logo? Or is something like this not feasible?

Maybe creating a custom package? I do that to apply the phone format fixes.

Exactly, thats the way. But if Maldaen considers using SSH a pain in the a**, that's even worse ;-)
Working perfect but you need to figure out how to create working packages.

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iPhone 3GS factory unlocked (3.1.2; Blackra1n, Cydia, OpenSSH, custom 3.0 ipcc file (no sig), tethering hack by Dev team, 32 GB)
iPhone 3G (3.0.1; Redsn0w 0.8, Cydia, OpenSSH) 16 GB