The company I work for makes the can your talking about (rectangular paint thinner type with screw on cap?)
It should seal just as well as a bottle
I could get into the science of osmosis and plastic but it really isn't a big deal
I'm sure both are fine.
The can shouldn't be used for longer then a year after it's opened but I doubt your fuel will last that long anyway.

PS
I use a plastic bottle
It what my fuel comes in.