I've never had a problem. I actually prefer the Trangia type bottles over the MSR or Sigg variety with the safety valve being the reason why.
Secondly, you shouldn't worry about your fuel bottle exploding. Heck, on long trips I used to re-fuel my Zippo lighter with stove fuel. And that lighter saved my rear end on more than occasion.
Thirdly, about the only thing you really need to be careful of with MSR stoves are flare-ups. I've singed my eyebrows a few times, it's an accident but it does happen. It usually happens when you don't prime the burner properly and it goes out. The trick then (not recommended but I do it anyway) is to turn on the fuel valve (the fuel should be in vapour form now) and quickly flick your lighter underneath of the burner to get it going again whilst at the same time moving your head out of the way. I know it sounds silly, but when it's below freezing and the snow is coming down in buckets, visibility sucks and you need to get some food into you so you can crawl in your shelter...it becomes a necessity.
Take it easy,
Adam