dd,
I have the same reservations about putting fuel bottles "in" a pack.
Had a bad experience my first year backpacking, bad O ring too :'(  So I bought and still use two large exterior pockets that zip closed. Each will hold a liter bottle of fuel, and rope/ tent/fly stakes/trowel etc.
 When I bought my GG food pack, it didn't have side compression straps. I had them added, and bought 2 more big side pockets for the food pack. Now fuel fits in them, in the big zip closed section, and fire starters/lighters/candles/candle lantern, go in the outside zip pocket.
 Since I use ALL synthetics, fuel and nylon/synthetic, don't go together very well ;)
 I like having the extra room and not digging in the pack for items I use all the time.