Scoring clarification for end of campaign/day of rest
The rules don't make the distinction between doubloons won and doubloons in your possession. Whoever wrote the rules probably didn't consider that someone might take this phrase extra literally. 

Logically it makes sense to not subtract the 10 starting doubloons because:

1) Like you mentioned, it doesn't matter either way and 
       subtracting doubloons each time is a completely unnecessary hassle.

2) You could end up with less doubloons than you started with. In this case you won't be able to subtract ten doubloons. Because it's possible to lose doubloons, it could be argued that any doubloons that you kept have been won.