One of use of "apparent" (likewise "apparently") is literal - the word means that something is observable. The other use is the opposite - it suggests that some people claim to have observed it, but you have yet to see anything convincing yourself. It could be described as a sarcastic use of the word, and often is said in a sarcastic tone.
When someone is sarcastic, their tone of voice and body language, as well as the context, usually tells you so. Likewise, the use of the words "apparent" and "apparently" are usually shown by their context to be either literal and sincere or not.
As a rule of thumb, if there is no need to say that something is apparent, then it is probably being used to cast doubt as in your example of "the apparent winner". If someone has been declared winner, that would not normally be in doubt. Adding "apparent" suggests that while some people have declared that to be true, others may still doubt it.
When the word is used literally ("apparent" literally means that something is observable) it is usually to clarify something that is already doubted by someone else.