Hiya, the AVID MOJO seems like an awful lot of beefy hardware for an Amiga analogue video signal. Was this a device you had to hand.
"Why its not possible to capture Amigas output in this quality too?"
If you were unable too resolve this issue, here are some workaround thoughts.
Are you trying to retain the best closest match of the original source to recorded file without degrading via say S-Video/Composite.
You could comprise and use the S-Video/Composite on a PC video card and record using
http://www.virtualdub.org/ for 95/98/ME/NT4/2000/XP.
Another option you could explore is maybe if you have a DVD recording device/player, plug the Amiga's RGB Scart into it, record the footage in HD to DVD then transfer the DVD material over to your PC workstation and edit and prepare this way with free GNU software.
This way the DVD recording resolution is already higher than the source thus retaining max Amiga video clarity and allowing for degrading/gentle compression from HD to something for comparative to the Amiga's video source.
I think too as you've mentioned and the other posters have followed up with regarding the actual compatibility and reliability of the conversion of the Amiga's RGB analogue signal to YUV too is part of your initial problem.
Also maybe try loading your Amiga demos into UAE and record them to file this way.
Just some ideas, hope it helps.