The loss is more in Draft slot $$$ then anything else #1 can always go underslot and pick up a ton of cash to spend on later picks.

Unless your top 3 pick is a Scott Boras client and he demands (and you end up giving to them) his full slot value, plus the total allowable overage before loss of future draft picks, and every other dollar you saved from all the other  draft choices you signed for underslot.   see Carlos Rodon, 2014 Draft overall pick #3 as an example.

Plus 9 times out of 10, an overall top three or four pick that signs for significantly below slot value is an "overdraft" pick.  An "overdraft" pick is a player that was rated lower on draft lists that was picked higher so the team could save a decent sum of his slot value to use on later picks.  The only overdraft/underslot top 3 pick I can think of that ended up a homerun was the Astros in 2012.  Holding the overall #1 pick, they passed on consensus top pick Mark Appel due to Scott Boras' pre-draft demands and instead took a HS SS from Puerto Rico (Carlos Correa).  He signed for over $2Million under slot and the Astros used the savings on his deal to land Lance McCullers and Rio Ruiz to slot-busting deals later on in the draft.