Put some alcohol on a flat metal surface outdoors, an old baking pan works. Light it. Most of the flame will be clear or very light blue and difficult to see. Where you do see yellow it is the product of incomplete combustion or contamination in the fuel or burner.On my non-pressurized stove it most certainly does not burn clear. I can definitely see the flame. Also, unless you fill the canisters while they are still hot (i.e., operator idiocy) refilling them is hardly a fire hazard. Someone who is that inept ought not to be sailing a boat!
I use an empty soup can with a small hole drilled in the bottom to fill the empty, *cold* canisters. I put the canister in the sink, set the soup can on top of the canister, and then pour the alcohol into the soup can. The small hole slows down the flow so that it will not overflow the canister. It's about an easy as can be and perfectly safe.
If you fill a canister in the sink you're much safer, filling a canister in the stove can allow some alcohol to spill and puddle in the stove or if you are sloppy it end up elsewhere where it will be easy to ignite. Best practice is to fill a cold canister outside in the cockpit.