Obviously I don't think software developers should be fired for rolling in at 8:02, but on my current team our start time is 100% personal preference, and the window is about 4 hours wide. If you added shorter schedules on top of the insanely flexible schedules, we'd basically have separate teams at that point.
Most places I think can only operate on one: shorter work days or more flexible work days. If you're going for the shorter work days, you need to be more strict about what time people arrive or it's a lot harder. Subsequently if you're super flexible about arrival and departure time, it's hard to maintain any team coherence unless everyone is putting in 8-9 hours a day.
None of this matters if the team is set up to handle remote work well and the majority of communication is written.
On your point on remote work, I don't really think this is true. One day response turnarounds can be a real pain in writing.
It strikes me that #1, #3 and a large part of #4 are not problems caused by the reduced hours but purely by the flexible hours. Do you think this system could've been more successful with more coordinated working schedules?
#2 on the other hand sounds like a systemic problem exacerbated by reduced hours, rather than caused by. It seems to hint at an imbalance in resource allocation in general, which is a problem worth addressing even with the increased hours.