The SEO friendly urls is a nice feature but i think it needs to be standardized ie some places separates words with dashes while others separates them with dots.
Having a nice tree of urls will greatly streamline the product like everything else
This way the user getting the link knows it is a forum link, and actually one of the threads, with that title. (and .12 helps keep it unique in case of the same threads).
The PHP functionality shouldn't be disclosed, and details of content kept to the page itself.
I was going to say the same regarding short URL's, but you beat me to it. I would LOVE if there were a permalink like system for the forums, as I prefer to do my own structure, rather then use a default one or one with low customization.
There is an option to remove the ID, for forum titles only. I think is the easiest way to deal with ID's, instead of other methods (i.e. current date).
I understand your logic. However, SEO url's were designed only for search engines, users really don't care how a link looks. I dare you to tell me how would be beneficial for Google to have search results queried and penalize you for cloaking links (same for members).