You should feel comfortable with either choice. However, factory finishing offers many nice advantages. Factory finished flooring is inspected for defects at the mill so you receive first choice every time. On-site finishing depends on the quality of the workmanship that day.
Factory finished flooring usually installs more quickly and without the dust and odors that are involved with on-site finishing. However, even though factory finished flooring comes in a variety of colors, on-site finishing allows for closer color match with existing woodwork or cabinets.
Both factory finishes and on-site finishes are available in either high gloss or matte. Both types have exciting new finishes developed with space age technology. These finishes are not like grandma's old wood floors because they require no waxing.
Prior to the development of engineered hardwood flooring, hardwood products could not be installed on slab or in your basement without a special subfloor system. Now you can enjoy real hardwood flooring in those areas without all that fuss and expense. A special cross-ply construction eliminates the problem of expansion and contraction usually associated with solid hardwood.
Don't become overly concerned with thinner or thicker top wood layers associated with engineered products because it's the finish you are walking on. Generally speaking you won't need to re-sand and finish these products; just re-coat them unless you need to change the color.