I thought about this earlier. I think that there would be extreme pressure from MLB offices if they were to offer underslot money and not sign him, but if they offered slot money (3.5 million) or a little more, it would be hard for the MLB to get involved.
As far as losing the pick is concerned, that only happens if they sign a player with a qualifying offer, which is in their control. And I am beginning to believe that they will not do so this winter.
I have no idea what next year's draft class looks like, but I am quite sure that our front office does, and can take that into consideration.
I think what it comes down to is if they think that they can sign their first choice this year for enough underslot to pick up a few good overslot players later in the first 10 picks. That strategy seems to have worked well last year, but this year's first pick has a lot less slot money to work with.
But even if it isn't their actual strategy, at least it seems as if they wouldn't lose much if anything if they for some reason can not sign their first pick.