In my opinion it is much better product when factory applied. It is done in a controlled enviroment in terms of humidity and temprature. In addition it is not simply applied with a brush but it is flood coated like a water faucet then smoothed with various brushes, thus more material actually penetrates the product.
Set the quality of the amterial aside for a moment, touch ups will be necessary on site when installing a prefinsihed product thus adding minimal cost over installing a bare or primed product. However compare that minimal increase to hiring a painter to paint the entire house... ON a 30 square house the cost increase to install all pre-finished siding and trim boards may be $2000 above primed price. However A painter may charge around $5000 to paint the same house.
When I tell my customers this, exactly as I have explained above, not one has ever opted for the painter to come in after I was done.
You can face nail if you want to. You are not supposed to face nail fibercement anyways, except trim boards etc... and we usually purchase color-match nails. Also we get the OSI Quad color match caulk and always always always buy a few gallons of color match stain for touch up.
Remember you can have the manufacturer install their paint and many states also have seperate pre-finish factories. I usually opt for the pre-finish factories because they offer a much wider range of colors and that sometimes alone sells the job. Another part of the reason I usually opt for the prefinish factorties is for the prefinished nails and color match stain. I've had a hard time matching some of the "stock" hardie and Certainteed colors.
So to summarize, there is no reason to paint new wood or fibercement siding anymore when you can get it done
better and cheaper than the "time tested" or "old school" methods of having a carpenter do the install and a painter do the painting.
P.S. Any painter will tell you to paint it after it's installed
you cant but you can 
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