Here's the deal (it's a little confusing to explain): The scale lenth is the total length from the nut to the bridge but that's not the end of it. The distance between the frets has to be proportionate to the scale lenth. So if you're neck and body don't match up, the frets end up in the wrong spots so you can't get proper intonation. They will either be too close together or two far appart depending.
And, by the way, just because your neck and body came from a guiat w/ the same scale lenth, doesn't mean they'll work together. I have a 25.5 inch scale guitar w/ a twenty four fret neck here. If I were to take that neck and put it on, say, a Strat, it wouldn't work. You see on the twenty-four fret guitar, the distance from the body to the base of the neck is slightly shorter but the neck is slightly longer than on the standard strat. It addds up to the same distance but each half is different.
Hopefully that didn't confuse you anymore.