The Catholic Church Against the Bible?

One of the most frequent criticisms of the Catholic Church is that She teaches Her members to trust Her,
instead of the Sacred Scriptures: that the Bible and the Catholic Church sometimes disagree, and that Catholics are forced to choose the Church over the Bible. Other variations of this argument are that we take “the Church Fathers” or “tradition” over and against Scripture.

To see why these arguments are false, consider four general propositions:

1. Scriptural Interpretation / Exegesis: “The Bible might seem to teach X, but it actually teaches Y.” 
2. Extra-Scriptural Tradition: “The Bible is silent on whether X or Y is true, but we know from Tradition that the truth is Y.” 
3. Church Disciplines / Practices: “The Bible leaves room for either X or Y policy, and we’re going to take Y.” 
4. Anti-Scriptural Teachings: “The Bible teaches X, but I want to reject X in favor of Y.”

As Catholics, we believe that it is within the Magisterial authority of the Church to do (1), (2), and (3). But we don’t believe that the Church may do (4). The Magisterium of the Catholic Church has held as much, acknowledging Her own limitations, in paragraph 10 of Dei Verbum, the Second Vatican Council's statement of the word of God (which includes the Bible and Apostolic Tradition):

Vincent Van Gogh, Still Life with Bible (1885)

Sacred tradition and Sacred Scripture form one sacred deposit of the word of God, committed to the Church. Holding fast to this deposit the entire holy people united with their shepherds remain always steadfast in the teaching of the Apostles, in the common life, in the breaking of the bread and in prayers (see Acts 2, 42, Greek text), so that holding to, practicing and professing the heritage of the faith, it becomes on the part of the bishops and faithful a single common effort. (7) 

But the task of authentically interpreting the word of God, whether written or handed on, (8) has been entrusted exclusively to the living teaching office of the Church, (9) whose authority is exercised in the name of Jesus Christ. This teaching office is not above the word of God, but serves it, teaching only what has been handed on, listening to it devoutly, guarding it scrupulously and explaining it faithfully in accord with a divine commission and with the help of the Holy Spirit, it draws from this one deposit of faith everything which it presents for belief as divinely revealed. 

It is clear, therefore, that sacred tradition, Sacred Scripture and the teaching authority of the Church, in accord with God's most wise design, are so linked and joined together that one cannot stand without the others, and that all together and each in its own way under the action of the one Holy Spirit contribute effectively to the salvation of souls.

So the Church lacks the ability to trump the word of God. But empowered by the Divine Commission, and perpetually guided by the Holy Spirit, we need not fear this conflict even as a possibility. Christ sent the Church out to teach the Gospel to the whole world (Mt. 28:19-20), and equips Her with the Holy Spirit to achieve the task He which He entrusted to Her.

Ironically, while Protestants criticize the Church for (1), (2), and (3), they end up doing each of these as well:

1. In correcting heretical misinterpretation of Scripture, you’re engaging in (1), showing that “The Bible might seem to teach X, but it actually teaches Y.” 
2. In saying that the (internally-anonymous) Gospel of Matthew was written by St. Matthew the Apostle, you’re engaging in (2), holding that while “The Bible is silent on whether X or Y is true, but we know from Tradition that the truth is Y.” 
3. And in deciding to have services at a particular time on Sunday mornings (and maybe Wednesday nights, as well), you’re engaging in (3): “The Bible leaves room for either X or Y policy, and we’re going to take Y.” 

The only difference is that we have a coherent ecclesiology that explains why the Church has the ability to do this. Protestants tend to deny that the Church have this ability, but are forced to do it anyway.

I don’t expect that this explanation will immediately dissolve all of the arguments against the Catholic Church. But I hope that it helps to put these arguments in perspective: are you complaining that the Catholic Church is doing something the Bible forbids? Or simply that She does something that the Bible (in your view) doesn’t require? And if it is the latter, how is that an argument against the Catholic Church at all?