Alex, I didn't say it was always noisier, but you have to admit that introducing any large AC signal that isn't the audio input into the box will invite noise problems - even control LFOs are subject to introducing unwanted artifacts unless very carefully implemented, and a big 50/60Hz current inside the shield just isn't a good idea if it can be avoided, especially for high-gain circuits. Congrats on doing the extra work to make it viable, but keep in mind that most manufacturers (even boutique operations) simply can't afford that kind of extra expense - after all, even if your pedal retails for several hundred dollars, the margins aren't huge, so you have to sell a bunch simply to keep body and soul together, and a few extra pennies on each unit really adds up!
As for everyone sticking to a standard power supply, the original fuzz effects were almost all positive ground, so if you want vintage mojo, you can't expect modern convenience.