Having studied my board and your I think I have some answers for you.
Your board is the earlier version so I am pretty sure they are Atari modifications, they have done this before on the Mega ST. Not very pretty but functional.
#1. Not sure but if it ain't broke don't fix it! Green was a common colour for atari to use for this as they blend in with the PCB colour better.
#2. The 74ls164 is for serial to parallel conversion. it is on my board U900 which indicates a late addition as the two IC below are U211(74ls04) and U209(74ls86). These two IC's are already on your board.
#3. The TOS normally controls the boot frequency and it normally depends on the language. So I would say it was due to the Eproms. As the board itself is a PAL version (U402 would be occupied and some of the parts around Y100 would be missing if it was a non PAL machine)
