The RCP is actually the most valuable chip on the board. The RCP then processes the data, performing intense floating-point operations. Some of the data is sent to the R4300i, and some of it is stored into memory. My guess is U2 because of the few of traces leading to it. If the value is sent correctly then access to the RCP to load data is allowed, otherwise some error is generated.
Encoding seems more complex than a simple boot sequence.
U4 could also be a decoder. Several traces lead to it, and then go to the RCP and U6. Perhaps commands to the RCP or R4300i are decoded while other data is allowed to flow freely. An example of data which is not encoded could be a matrix whose numbers the RCP is going to crunch. There could be certain command lines which need to be decoded before a game will function.