I have a couple of things to say about this!!
Why do you think there is a problem with the MAI chip. Maybe the technicians for the Pegasos and MorphOS did not use this chip properly!!!!
I don't know the layout of the Pegasos and other used components but maybe some components are used on the Pegasos that aren't used on the Teron and are causing these problems.
Maybe some of these problems were caused by to much intervering with the reference design
Who knows! But why should this be true??
Give AmigaOS some time!! In the days of Commodore is was said that a straight port of OS 3 to PowerPC would probably take 18 months. This is not a straight port and the BIOS problems caused some interference.
Let me also remind you that there is no hardware design completely faultless. The VIA 686B southbridge has a known problem which is patched by the VIA software drivers on the PC.