Do you believe the free agent market works - as a market? If you do, then you have to conclude that opt-outs are granted in lieu of higher guaranteed dollars... that the total compensation package offered and accepted is market-clearing.
If you think the market is failing here... you're arguing that the players somehow have obtained market power over the general managers?
Put another way: If the Phillies' front office believes that opt-outs are unacceptable, and a given player's agent demands an opt-out, the Phillies' front office can respond, "Pound sand," and hang up the phone.
If instead, the front office sees opt-outs as a concession to the player, then they respond with, "OK, but that will cost you $5 million/year for the last three years of the contract," or some such.
I find the argument that "there is no point" to opt-outs to be a bit silly, frankly. If it's something of value to the player, it's something that can be negotiated against other things of value (read: dollars, no-trade clauses, guaranteed outyears, player options, etc., etc., etc.). You can argue it makes the negotiation more complex - but it also increases flexibility. You can argue that it makes long-term roster management more complex, and I would agree - but I have to think that front offices will develop strategies to mitigate that.