Hi Dorian,
AdWords allows multiple final URLs specifically for the use case where you are not including lpurl in your tracking template. For example, if your tracking template is directing traffic to a tracker that redirects some traffic to one URL and other traffic to another URL, e.g., for a landing page experiment.
If you do have multiple final URLs and you are using a tracking template that includes lpurl, AdWords will simply pass the first final URL for the lpurl parameter value. Also, if you have multiple final URLs and you are not using a tracking template at all, AdWords will simply serve the ads with the first final URL as the destination URL.
Currently, the UI does not support adding multiple final URLs, although you can view additional final URLs by hovering over the callout to the right of the Final URL entry field, at which point you'll see an Additional final URLs tooltip that shows the 2..n final URLs.
Regarding reports, the semicolon in your CreativeFinalUrls will not be escaped. However, it does appear that there will be a space following the semicolon delimiter, e.g.:
"AD_PERFORMANCE_REPORT (Apr 22, 2015)"
Ad ID,Final URL,Impressions
Cheers,
Josh, AdWords API Team