How to set the double-click speed in Lion with a multi-touch trackpad

Sadly, I don't think it's possible to do that without a third party solution. Two popular applications that allow you to tweak the touchpad and mouse are Magic Prefs and Better Touch Tool.

You can rule out SteerMouse, I just connected a second mouse and there is only one setting for double-click delay shown. Based on that I'm doubtful of USB Overdrive's claim: "The USB Overdrive can easily handle several USB devices at once and can assign different settings to each one." - but it's probably worth a look!

I think ControllerMate could do it if the developer felt like it - it's a way more configurable approach and is flexible enough to build complex control schemes for HOTAS game controllers. You should register your interest in being able to control the Magic Trackpad with a quick email. I don't know for sure that ControllerMate can't do what you want, it all depends on whether its building block approach sees a "Source" for each mouse-like device or whether it just uses the kernel's mouse driver output and sees an aggregate of control input for the two devices. There is a time-limited trial available.