You're the consumer - if you want to leave some steerer above the stem for future flexibility (or lack of flexibility!), that's your prerogative, and if the shop done agree, then take your fork (which came from Felt, not the LBS) and go elsewhere. Having the steerer extend above the stem is irrelevant as there is no torque exerted on that portion of the steerer. The important thing is to have the expander plug support the portion of the steerer clamped by the stem, and the length of the extension above the stem is limited only by the length of the screw connecting the top cap to the expander plug, necessary to preload the headset bearings. Extend the steerer as long as you like, as long as you can find a sufficiently long screw.
All that being said though, I had a 10mm extension above my stem for years, for "future flexibility", until I came to the conclusion that I wasn't going to be raising the stem any time soon, nor was I planning on selling the bike ever, so I cut off the extension, and the bike looks much nicer. Sometimes it's OK to prioritize the actual now over some nebulous future - and screw "the next guy" - that'll be his issue.