Interesting.
Only thing I can think of is the perhaps the depth of the starnut/anchor in the tube in relation to the stem.
Lets exaggerate the issue: what if you had say, 1 foot of tube above the stem? Not seeing how it would affect stress on the tube below the stem. Well, unless your stem was 1 ft above the headset. Sounds like Felt doing some CYA.
I'd have the LBS install the race on the fork and install myself.
I'm with you, I always leave a cm or so on top for the next guy even though there never seems to be a next guy.