I am assuming you used a lens to do the magnification BEFORE the light hit the camera sensor. This magnified the subject 100X bigger than could be seen with the naked eye. If printed to scale of your image, it would be 100X bigger than actual size. If printed half size, it would be a photo taken at 100X magnification, printed at a size that is 50% of actual. You would likely still see detail available only at 100X magnification, but it would not be printed at 100X of the actual size.
Here's another way to look at it. When you take a photo of your Land Cruiser, you might get an 11 x 17 print made of it, but you probably wouldn't print it ACTUAL size -- you'd have an enormous photo. But if you did, then you would have an actual size photo at 1X magnification.
Now let's say you took a 1" square photo of the door hinge, at 100X magnification. That would be 300" x 300" = 25 feet square if printed ACTUAL size. If you printed it at 5" square, that would be a photo taken at 100X and shrunk 80% in the printing. It would still be 100X magnification, but it would only be 20X actual size.
Clear as mud? Few things are printed at actual size, unless you are buying from Fathead.com
. I agree, it's a confusing issue.