Qualifying is a tricky business at the best of times. Having qualifying just half an hour after FP4 – that is, if you don't have to pass through Q1 – makes it even more complicated. That final session of practice is the only chance to work on setup without worrying about getting through to Q2 – and in my book, makes it the most interesting session of practice all weekend. But that also means that if you want to compare two different setups, FP4 is the session you do it. After FP4, you have thirty minutes to get two bikes ready for qualifying, with identical setups.
There is little room for error. Should you, say, crash in FP4 on the bike with your preferred setup, as Marc Márquez did at Motegi, then it makes qualifying complicated. Even if you get the bike back to the pits quickly, your team probably won't be able to get the bike back ready to race in time for the start of Q2. And if your second bike uses a very different setup – some combination of a different rear link, a different offset, different rear shock, say – then your team might not have time to change it all back again to the way you want it.