I think generally across Europe the dropout rate is quite high for medicine and my theory for that would be that it is relatively easy to get admission to these universities. US and UK all have very lovely graduation rates and that is because they admit very capable individuals by setting high standards and entry requirements, whereas I think all you need is CCC for Czech universities (imagine someone guessing the entire entrance exam & being admitted, of course they will struggle lol).
For Palacky what additional costs are you going to save? (just asking out of curiosity, I withdrew my application from so can't go anyway)
Masaryk has extremely poor graduation rates. If I can remember correctly only 20-30% graduate. Historically, Charles was also something similar (with poor graduation rates) but magically more people seem to be graduating recently (currently HK seems to have the highest graduation rate out of Czech Republic). I think Palacky isn't the greatest either but it isn't as bad as Masaryk, I think it would be similar to first faculty (maybe because it may be easier to get accepted there?). The second faculty of Charles has hilariously bad graduation rates, like only 20 people graduate each year irrespective of the amount of students admitted, not sure why though. I've heard people say that some universities accept a lot of foreign students (as they pay more) and design it to be difficult so they pay the money initially but the university itself lacks the facilities to graduate the hundreds of students they accept, which I think is the case for Masaryk and the second faculty (I don't think it is the case with the rest though).