I'm planning on going to Japan, buying a strat and bringing it back with me to Australia on a plane.

I will be buying a new case with it, and i'm trying to decide between two gator cases,

1. Fit-all polyethylene ATA case http://www.digimart.net/inst_detail.do?instrument_id=DS00146935
More info at http://www.gatorcases.com/productsmodeldetail.aspx?LID=2&PID=5&MID=42

2. Moulded ABS case http://www.digimart.net/inst_detail.do?instrument_id=DS00146925
I can't find the moulded model on Gator's website, but here's the overview http://www.gatorcases.com/productsdetail.aspx?LID=2&PID=7

The small price difference does not concern me. Obviously the first option has a tougher exterior (apparently it can withstand 3000 pounds), but the interior is not moulded for the strat like the second option.

What is more important for a case that I'll be checking in at the airport, exterior toughness or snug interior fit?

snug interior fit. no point in having a tough exterior if your strat is going to be banging around on the inside.
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if you're sure you're going to get a strat get the strat shaped case, but if there's a chance you might get something else get the unmolded case
I would go with the molded case because you know what guitar you want to get. The more snug the fit is the better, I would put some towels to make your neck doesn't move too much. Might want to check google I found some interesting ways to take guitars on planes, like this one guy apparently disassembled his strat and packed in with his clothes x_x, flew all the way to turkey and everything was ok. Bit too much of a risk for me personally.
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