one instance per particle seems inefficient but most computers can handle it, especially if they don't collide, and it gives you a ton of fun flexibility (using an emitter to spawn a flock of enemies, for example, or emitting particles that then emit more particles, etc).
Tiles however are NOT a collection of unique instances, they are blitted relatively efficiently. They do use a single instance of an empty collider to do the actual collision check, but otherwise they're pretty fast.
BUT that's not to say that flixel is not a work-in-progress with a fair number of broken or unoptimized elements :) I have a list of...oh I guess i'm down to about 20 things that have to be fixed or revised before the next big public whatever!