Depends on how the particular school approaches PBL-style learning.
At Ohio U., the now-defunct PCC track was a PBL-style curriculum. We were not "taught by a textbook" but by PhDs and MDs/DOs, and the curriculum was problem-based. For example, instead of learning physiology by sitting in a classroom listening to lectures, we would meet in small groups and have clinical cases ("problems") that we had to solve that would teach us concepts of physiology. Whatever gaps in our learning were closed by self-study supplemented by lectures if needed (we could request lectures if the topic was too difficult to learn by self-study).
Again, my experience is only with Ohio U. We were definitely well-prepared for clinicals as we could easily integrate all the basic sciences with real clinical cases (this is the strength of problem-based learning), and we had no problem with Steps 1 & 2.
My advice would be to investigate PBL-style curricula in the context of the particular school you're interested in instead of in general terms, as every school does it differently.