You won't be penalized anymore than you would if they crawled the UBB and found the URLs on their own; the script feeds them a URL and their crawler will hit pages that are linked off of that page itself to build its real index.
If you follow the example in the readme on what to give google it should actually build the URL the same as what you posted (as form link); the sitemap can be customized to build just about any format of url in just about any type of sitemap you'd want. The recommendation however is to build the sitemap as:
ubb.sitemap.php?type=1&se=2&offset=0
Which will build links as:
http://www.yoursite.tld/forum/ubbthreads.php?ubb=showflat&Number=49643You could use:
ubb.sitemap.php?type=1&se=1&offset=0
Which would build links as:
http://www.yoursite.tld/forum/ubbthreads.php/ubb/showflat/Number/49644Currently we don't have an option to build with SEO urls or the fake html extension; we just have se friendly urls and standard urls (which likely will change in the future).
The script primarily aids SE's by feeding content urls to the SE, it'll continue to crawl URLs as it finds them (specifically on links you feed to them), it'll build "new page" links and other links off of the pages your sitemap feeds into their systems.
What I'd like to see is possibly have the ubb gracefully forward URLs with a redirect (301/302 header) based on what URL schema the user chooses in the UBB we could eliminate duplicate urls alltogether (as any url accessed that wasn't on the default selected would send a redirect like what the redirector scripts do); but I'm unsure as to how easy/difficult that could be.
