The Phillies would, and have in the past, done this even when there was no penalty (see their view on bonuses to international and draft amateurs in the absence of anything stronger than a suggestion from the commissioner). Despite being a wealthy team in a large market, the Phillies have always been among the most committed culture warriors in supporting the commissioner's efforts to hold back the tide of rising bonuses and player salaries. I think it's a class thing or an ethnic prejudice thing, rather than a money thing. Perhaps it's how old mainline money looks down upon kids from lower middle class backgrounds and looks down even more upon kids from Latin America or American minorities. Going way back, the reason Ruly Carpenter sold the Phillies is that he was so opposed to rising player salaries ruining baseball. To continue that good fight, he chose the nearly broke Bill Giles to form the partnership to purchase the Phillies, believing that Bill could be relied upon to continue the fight against the uppity kids, agents, and players.
Then Bill Giles frugality, in a financially strapped initial partnership where his ability to kick in more money, limited spending, set a tone of spending for the post-Carpenter Phillies. He cost the Phillies a #2 overall pick in the draft to wage the good fight against Boras and JD Drew. He even declared that he drafted Drew 'for the good of baseball', rather than allowing him to fall down the draft board to a team willing to pay his asking price.
The Phillies have always shelled out $ for players they viewed as 'worthy' of the money -- a declining Pete Rose, the post-WS Daulton and Dykstra, Thome, Lee, Harper, Wheeler, Realmuto, Schwarber are all guys the owners could see as deserving of joining their ranks of the local wealthy.
