After discussing it on the WiX mailing list, this definitely requires a change to WiX.

Currently, as soon as you include any per-user packages in your bundle the entire registration is forced to per-user regardless of whether or not they are ever installed.

I'm going to propose a change where the bootstrap application can assert that the bundle should be registered for the whole machine, so that when we start installing we can correct it. Can't be sure it'll be available for 3.5.1, but some time in 3.5's lifetime we should get this fixed.