You're right about some batterytypes liking to be charged with pulsed voltage; I've built a batterycharger once, and when it was finished, I heard that batteries should be charged with pulsed voltage; rectified AC, unfiltered (no electrolytic caps) should do the trick, if you can limit current & overvoltage.

As far as a 3phase machine providing 3 separate single-phase voltages; this can be done if you have 6 wires coming from your alternator; i.e. 2 wires per phase, and none of the 3 phases internally connected; i.e. 3 completely separate phases.

Then you can individually rectify them and end up with three single phases; however, if you don't load all phases about the same, your alternator will see a lumpy load (vibration, etc.).

Perhaps you could also use 3-phase star, where you use 4 wires: 3 phase wires, and the '0' (zero) from the center of your phases. That's the way the utilities provide electricity: they produce 3 phase, but each house normally only gets 1 phase (& other wire being the common 'zero' of the star). Unless you have a 3phase electric connection, obviously. Since most houses use about the same power, the 3phase system is equally loaded (what goes for your little genny about 'bumpy-ness' also goes for the big one from your power company).

Like I said, I'm not sure whether in a 3phase star-situation (with extra 'zero' wire) you could individually rectify each phase; when each phase is completely separately available (6wires) you can.

Hope this is a bit clear; my explanation won't win a prize for clarity, I'm afraid.