After making some phone calls and doing a scan through Google (thanks Dave), it appears that this is 100% normal. I'm not sure how many know that there are actually TWO versions of the 4.6 liter (I have another thread on this). One was made in the Windsor plant, the other in the Romeo plant. The Windsor plant makes truck engines only (4.6 and the 5.4). The Romeo makes car AND truck engines (4.6 only). The heads used on the Romeo's will not fit on a Windsor motor or vice versa, which is where I got my info on not being able to interchange the two (Mustang crowd). There is a difference in the number of valve cover bolts I was told, but have not seen it with my own eyes.
Since my truck is a Windsor 4.6 and it is made in the same plant as the 5.4 Windsor, they are indeed interchangeable. In fact, some 4.6's were equipped as such from the factory.
On a side note, one of the 4.6 versions is a 278 cubic inch rather than a 281 cubic inch. I want to dig deeper on this.