The folks that are selling the DVD version HAVE confirmed that DVD 1 in your DVD drive will be necessary in order to run MSFS. This slows down multiple installs.
And now your Windows registry will have no idea where FSX is located. Some add-ons look at the registry for the FSX location, so this is not a good idea.
There are no feature differences between the boxed set and the digital download of the same version. So you are getting the exact same thing for your money.