I thought that apart from leaving aside some things to the domain of metaphysics, they could've had a semi-plausible explanation of a number of things. Since the island was shown to have a core of extremely high electromagnetic activity that caused the plane to crash in the first place, they could've shown that to be the reason for the island having a warped spacetime. The flashes could've been portrayed as times when wormholes were generated which connected different spacetimes. Once the donkeywheel was fixed in place, this didn't happen anymore and the bunch was stuck in the 70s until the subsequent flash and the second plane crash. Due to the extremely warped spacetime, the clock time on the island would go really slowly as compared to the clock time in the present world. One can only guess as to what it is like in such a region of spacetime and that would've given the writers considerable leeway as to what they could get away with transformation between states of matter (smokey).
The explosion of the bomb would've been a good shot at what might happen if one was faced with the Grandfather Paradox and if that would prevent the course of events from the time cone from that point on. Also, it would've been a good take on what happens when a tremendous amount of energy is released at the source of a tremendous electromagnetic field. The bunch could've lived a lifetime on the island which had a slow time clock and still this lifetime might seem like a fraction of a second in the real time during their flight on Oceanic 815.