so how can this be done, 'make' USU create identical links?
No idea, it's just an "option" only in the general that with open source anything is possible if you are prepared to throw lots of time an money at at. In all cases one has to decide if it is justified....

are you suggesting adding hundreds of url redirects in an htaccess file?
Nope. That's another "option" that sounds nuts.

last time I looked at the CEON website the CEON Mappings Manager was no longer available
Contact them directly. They have the code, which is being reworked to a completely new animal. Convince them to take your money!

Or bite the bullet/take the (hopefully temporary) hit and use a solution that is supported here/revert to native urls.

I think your case illustrates what many people think, better to not fix what is not broken (the native urls) or you may get in a SEO mess when you want/have to change something.
I only use friendly urls to paste into emails and because it looks better/more professional to the browsing customer.
I don't worry about SEO, I consider that out of my little hands: I let Google invest their time and money in getting relevant search results from my unique, well-written, html/css correct content, irrespective of the url that locates it.