As to your concern about alignment, if you leave the knuckle on or take it off the car, it should NOT affects alignment settings.
As to type of bearing, the reason for my main point about bearing type in my reply are as follows.
The earlier year Rio uses 2 complete bearings that must be replaced on each knuckle, and later years use a single type bearing (with the outer race containing the actual ball bearings and inner races). As I stated, I was not sure of which type yours was equipped with.
From the sounds of your question and info you relay from service manuals, you should be able to "handle" the task, Good Luck and let us know how things go when you get done!
While my auto maintenance experience is still fairly limited, I have done pretty much all the maintenance work on my several road bikes for as long as I can remember (going back to when 10-speeds actually had only 10 speeds--my current "10 speed" has 30 speeds!). That might sound like a silly thing to say as cars are obviously vastly more complex and difficult to maintain than human-powered bicycles, but there are various components, techniques and approaches that the two have in common that translate well from one to the other.
In this instance I'm referring to bearings, of which I've installed and maintained on all my bikes, both the sealed and serviceable kind. I used to have an old Trek that had only the older, serviceable kind of bearing, on the wheel hubs, bottom bracket (where the cranks go) and headset (where the handlebars/stem connect to the fork and frame). Every year or two I took them apart, cleaned them thoroughly, replaced the ball bearings if worn, repacked them with grease, and installed them back on the bike. This also involved properly pre-loading them so they wouldn't be too loose or tight under use.
I assume that by "2 piece", you're referring to this type of bearing, not the sealed "1 piece" kind that is usually not serviceable and you basically keep on until it's worn or breaks, and then you just replace it with a new one. Internally there are still inner and outer races, ball, pin or roller bearings, and grease, of course, but they generally can't be serviced. If so, then my 2nd Gen 2010 Rio has the "1 piece" type of bearing. My current bike has these types of bearings, and they've done well by me over 12,000 miles of riding and still run smooth.
Anyway, thanks for the help, and I'm glad to hear that the 2nd Gen Rio's front wheels don't need an alignment even if the knuckles are taken off and put back on. That'll save me $70 plus tax, or just a bit more than the cost of one of the new hub/bearing/clip/nut sets I bought (I figured that with over 150k on the car and the bearings having needed replacement for at least a few thousand miles now, it was best to play it safe and replace the hub as well). I assume that that's one of the features that makes the Rio so inexpensive to buy and maintain, relatively speaking (even if there's probably a tradeoff in performance or ride quality).