There's no such difference in the case of Daggerfall. In the case of Arena I think it was the CD or the floppy release. Daggerfall was obviously only released in CD. There's one release, both before and after it was made free, the content of the disk and your DFCD folder should be the same I think.
By the way, whatever disk you install from, you should patch afterwards, because I think a patched CD was never released. You can find the patch in the extras sections. From what you say it seems you followed the instructions provided by Bethesda at the time of the freeware release, in that case you're cool too, since they included an instruction to apply the patch.
An image file contains a number of "metadata" beyond the files itself (for example the disk label). Sometimes a game might check these data, other times disks contain non standard metadata and even a normal image won't work (specially for copy protection purposes). Daggerfall doesn't perform sophisticated checks on the disk besides the label.
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