Since the mastery approach paid such close attention to readiness, prerequisites were better thought out. The prerequisites for literature at a certain level were not merely lower levels of literature. They also included the study of history, languages (Latin first, then Greek), rhetoric, and so on.
There's no single, objectively correct sequence, even for STEM subjects. But a master teacher can learn from experience what should be learned first, and to what level, to make a student fully ready to learn any given thing. Then take many experienced masters, put them together, and have them carefully work out a prerequisite tree from which they derive a sequence of instruction.
Another concern is that while a mastery-based education system could be wonderful for middle/high-performing students - it is likely to lead to a huge mass of underperforming students in the lower and middle grades. "Oh, you haven't mastered exponents; Then, you cannot move on to...". The reasons that these students fall behind may have nothing/little to do with their classroom experiences and yet they would not be allowed to advance. Considering the costs - there is no way we're prepared socially/fiscally for a huge backlog of low-performing students in these grades (particularly when they begin to drop-out en-mass once they get tired of failing at "little kid work").
At the extreme, if you refuse to move a student forward to higher-level content are you impeding their right to an equitable education as their peers? There is civil rights precedents for this question with regard to special education students being refused higher level academic work because they could not (by some metric) prove themselves "competent" to move forward.
Further, is the content we require our students to learn truly necessary knowledge for adulthood? It had better be if you're going to refuse moving an 18-year-old to the eighth-grade because they cannot write a "properly" formatted paragraph.
I agree completely that this is problem, but unless we decide that fully educating every child is the actual, explicit goal of compulsory education - and accept the significant costs that will be associated with that goal - then there will always be a purge valve for underperforming students. Currently, that is moving them along despite low performance and obvious gaps in knowledge/skills.