Probaby better to go straight in the mouth-but i cant find any evidence for this. My LO will not take by the mouth and it stresses her out so we put it into the bottle and love the way it stops any air bubbles being created in teh bottle and therefor not going into her tum. LO is pretty fussy-wont take water, etc, but it doesnt seem to bother her in the bottle-only half a mil anyway. Simeticone is verry inert and not absorbed by the body or broken done by the milk so should not be a problem in the bottle.
But, if your LO will take it by the dropper then do that-as they dont allways finish their bottle!