Re: ISP programming header on v1.2?
Having just accidentally tried it, I would strongly recommend you don't try reprogramming in-circuit via the 6-pin header. Not only did it not work, but it left the chip corrupted, requiring me to pop it out and reflash it.
However my main concern in this situation is for the LEDs and transistors, since they would see high continuous currents if the programmer holds the MOSI line low, which it might well do. I've noticed subsequently that the LEDs in each pair are quite different in brightness. Perhaps that was the case before ( without base or collector resistors, slight differences between individual transistors and LEDs could result in the current being shared quite unequally) or perhaps it is a result of this failed in-system programming attempt. I don't know, but If there is ever a v1.3 I would like to see a few more resistors. Having said all that, it still works ...
If it's really important to you to be able to reprogram in-system, I would suggest installing some single-pin sockets into the R1 and R5 (or LED) holes. Then you can just pop out those components to isolate the chip from the rest of the circuit. Just get one of the nice type SIP or DIP sockets with the round holes and with an X-acto knife carefully liberate the individual metal sockets. These are well handy for prototyping where you want to be able to easily change out individual resistors, caps etc.