People need to remember that gender and sex are two different things. Gender is between the ears and sex is between the legs. Gender is not binary it is fluid hence the term gender fluid and is sex really is not binary either, since there are intersex people. Also, when Tom is in the persona of Conchita 'he' is then referred to as 'she' just like Dame Edna or Ja'mie (who is played by Criss Lilley). You refer to Ja'mie as 'she' and Chris as 'he'. Simple.
ITT: people use definitions which only fit their preconceptions, ignoring entire fields of study in sociology and psychology, and miss the entire point of drag. It's like insisting on calling pantomime Peter Pan "she" because he's played by a girl, or calling Mrs Brown "he" because rawr penis. Conchita Wurst is a character - issues of gender aren't even relevant.
On a wider note, I honestly don't understand how some people on this forum just can't possibly comprehend that there's a difference between gender and sex. The analogies to race and species fail because it fundamentally fails to understand what gender is. Race and species are physical and genetic characteristics of a human and organism, respectively. Gender identity, unlike sex, is a sociocultural and psychological issue. What underlying biology that person has is not relevant to the discussion.