Well, the two recordings are difficult to compare directly because it was two very different organs and very different concerts. Pamadu is pretty much right.
First, I had a decent amount of time for preparations of the concert in Riga, and during the concert I had
two "registration-assistants". The organ in Riga Cathedral (which is one of the finest german romantic organs in the world) can not be compared to the organ in Assisi, which was unfortunately in a very bad shape (missing notes in some stops, slow pneumatic action - long delay from pressing a key to hearing the sound - etc.).
As for the concert in Assisi: When I sat down and played the Toccata, I did so without having touched the instrument before and making the stop changes while playing, guessing, using my experience and knowledge of organs in general. It was not a solo concert, but rather a concert featuring the Cecilia Choir (whom also had their own organist, Klaus Jerndorff, to accompany them). I just played for the fun!

Still, I felt that my rendering of the Toccata and Fugue that evening had a certain "touch" that represents a part of my vision of playing Bach (and other music), thus I decided to post it on the net even though it's very "raw". But it can not be said to be generally representive of my current way of intrepetation due to the circumstances.
What people (who are not organists themselfs) don't know is just
how big a difference there is between the different organs around the world. I would say that - even if both were in equally good physical condition - the difference between an organ like Riga (tracker action, 124 stops) and the Assisi organ (pneumatic action, 15 stops) is just as big as between a piano and, say, a harpsichord (they both have keys and strings and that's about it), if not even bigger! The two simply cannot be compared and the playing style will have to be adapted to each instrument. That's part of what makes the organ so fascinating and challeging in my opinion.
To make a real comparison between the young Frederik Magle and the "old"

I would have to do a new recording of a "big" concert with rehearsal and preparation time on a great cathedral organ, like the one Riga. Hmmm... Perhaps I should go back one day, maybe make a CD....