I've some good news, and some bad news.
Creation of the initial seed is not complex, it's not even a formula needed.
How does it work? After some more debugging i found out that the
initial seed gets copied from 0x04000104 to its final position in memory (0x02020000).
That adress is the counter of the GBA timer 2/4, which is running @ 256Hz; 65536clks.
More about those Timers can be found here
The timer starts counting when the screen changes to the "Press Start"-Screen.
This is initiated by the first button press or waiting till intro is finished.
Once it started counting, it will do so until the initial seed has been determinated.
A soft reset will have the same effect as if you switch off the GBA.
Also this explains my captured initial seeds. The low ones from frame 1 to 48 had no
other instructions at the moment the first button was pressed.
The ones after that have a routine running which takes some cycles and therefore increase the counter.
I think it will be almost impossible to get a desired initial seed, tough you
can get some equal with the help of autofire. The clock of the timer is imho too high.