Hey Eli! Question…since the Roman Catholic rejects what God has revealed in scripture as the final authority (Sola Scriptura), couldn’t we (presuppers) also challenge the knowledge claims they make?
It needs to be made clear that Roman Catholics affirm the authority of God’s Word. It is the authoritative place given to sacred tradition that a Protestant who affirms Sola Scripture would take issue with.
To place this question within the context of presuppositional argumentation, I take this question as coming from the idea that since we (presuppers) argue that unless the Christian worldview is in fact true, then knowledge and intelligible experience would be impossible. I suppose the question is asking that since Roman Catholicism is antithetical to the genuine Christian faith, does it fall prey to similar internal critiques that we could offer against the atheist, agnostic, Mormon, Muslim, etc.? In other words, does Roman Catholicism provide the necessary preconditions for intelligibility and knowledge?
The presuppositional procedure against the Roman Catholic will be the same as with the atheist or any other form of unbelief. That is to say, we will want to follow the “answer not the fool, answer the fool” (Proverbs 26:4-5) methodology. In essence, we do not want to answer the Roman Catholic after a fashion that suggests the intelligibility and biblical support of their professed authority (Bible + Sacred Tradition) (Don’t answer the fool), yet, on the other hand we will want to hypothetically grant the truth of their position and show where it leads (answer the fool). This could be done in a number of ways, but I think the most useful way is to find common ground in the scriptures.
If the Roman Catholic position is that the Bible is authoritative and it is in fact the Word of God, and Sacred Tradition is equally authoritative, then the presuppositionalist will want to find internal conflicts between the teaching of scripture and that of Sacred Tradition. If the internal conflicts can be demonstrated in the twin authorities of the Roman Catholic worldview, then it will have been demonstrated that the Roman Catholic position does not in fact provide the necessary preconditions of intelligibility and knowledge (Because its fundamental pillars are in conflict), since any worldview that competes for being the necessary preconditions for intelligibility must itself be intelligible and non-contradictory at its most fundamental level.
Now, all that said, Roman Catholics will have various responses to the Protestant attempt to show these internal contradictions and that’s o.k. Using a presuppositional approach does not make apologetics easy. The Protestant will still have to familiarize himself with the Roman Catholic position. The Roman Catholic won’t simply stand there as you ring off a bunch possible internal conflicts within his own worldview. Expect responses, listen carefully, and respond biblically, logically, and with gentleness and respect.
If you engage in such an interaction respectfully, then perhaps there will be further opportunity to share with the person on a different occasion. Part of doing apologetics effectively is having a long game. Do not expect the unbeliever to fall down at your feet after simply hearing your case. Human interaction is complex and often messy. Be patient, loving, and adaptable praying that God blesses your efforts by opening the heart of the other person to receive the truth you are giving.
 This is simply to say that we do not begin the discussion from a position of neutrality, a “no one knows as of yet” mentality.  Common ground is not to be confused with neutral ground. There is no neutral ground between genuine Christian faith and unbiblical counterfeits. A good common ground between the believer and the Roman Catholic is their shared belief in the authority of the Bible. While they reject the Protestant position on Sola Scriptura, it is still a fruitful endeavor to appeal to scripture nonetheless.