I use both.
I like using the piloted holder, tapping from the spindle right after drilling the hole, before unclamping the part. It assures the best alignment with the hole.
With the piloted holder it is still possible to bend the tap or thread at an angle because the pilot is not zero play. So you need to be sure the spindle is in alignment with the hole, and you keep your force symmetric around the axis of the tap.
The big Phase Two tapping fixture is very handy indeed. It is fast and is great if you have a bunch of holes to thread. It also has a stiff spindle with zero play, reducing the possibility of threading a hole at an angle. Its one draw back, IMO, is it probably abuses the tap a little more than the other arrangement, perhaps making it less ideal for tiny taps. It is still way better than nothing, but the piloted holder is better when you use it right. Certainly cheaper.