Two things.
First, with one rag joint or one u-joint, you can't really do much for alignment. And that's all you get. It's best to do what you can do to align the steering column to the box. I don't think it's all that difficult unless you have a "problem car" - i.e., a bad rust bucket or collision damage.
Second thing, and I've never done one without a rag joint so I don't know how bad it is, you will get some high frequency vibration from the power steering pump up through the column, if you use a u-joint. Back in the old days, guys would weld a shaft on a 605 to emulate the stock box/column. Those had that vibration. CCI sold 605 conversions that way, but quit doing it, instead using shortened columns and rag joints.