Interesting, anecdotally, I went to three different universities and they all barred this from happening without an explicit override from a professor or occasionally an adviser. Just curious what experience you have that makes you say this?
Also, at least when I was an undergrad, the Banner student system (from ellucian company) had no system in place for barring you from registering from classes. This was frequently the point of discussion between the professors that I TA'd for.
As one anecdote, they once told me I needed to retake intro physics. On the pretest given on the first day of class, I came within one problem of a perfect score. Didn't make a lick of difference - their syllabus differed from the last university in the most minor of ways, and despite the fact that the class never actually covered even 50% of the stuff it claimed to on the syllabus, I was made to retake the entire sequence anyway.
Although I think your situation was pretty special as well, transferring universities is usually incredibly annoying and filled with road bumps. I've found there's a lot more leniency given to students who remain within the same university.
The way to get around this isn't by taking pretests (which don't mean much) it's by writing the final exams. In some institutions you will be able to do this without (full?) course fees if you are attempting to demonstrate equivalence.
Do they accept credits from any other institutions? Isn't there a national agreement on accepting credits for certified degrees?