The 5.4 has a different deck height it is not a stroked 4.6. Different block all together.

The 4.6 Ls bore and stroke are nearly square at 3.552 in and 3.543 in respectively. Deck heights for all 4.6 blocks are 8.937 in.

the 5.4 Ls Bore diameter is 3.552 in and stroke is 4.165 in, the increased stroke necessitated a taller 10.079 in engine block deck height.

So the bore is the same the stroke is different and because of the stroke the deck height is much much higher on the 5.4 block.