I think Klentak had a reservation price for each player, had a term limit on Machado (probably to be able to trade him if things went South), and wanted a long-term on Harper (i.e., planning to make him the centerpiece).
Klentak held his ground, was patient, and got the one player at his reservation price (i.e. $330M however it was spread over a contract).
Obviously, they value Harper higher, because they could have signed Machado for $330M or less.