I am using a USBasp clone to program a ATMEGA328 which is on a broadboard with a crystal/caps, through the IDE.
I put a LED on IC PIN 19 (which would be Digital 13) so I could burn the blink sketch and confirm this has worked. Using the IDE, I use "upload using programmer" and sure enough I get the LED blinking. But at this point the USBasp is still connected. PIN 19 is SCK on the programmer, so doesn't it cause a problem blinking the LED on this pin, as this is sending HIGH back to the programmer? Likewise, if I was programming a different sketch that was using Digital 12 & Digital 11, it could also be sending HIGH on the MISO and MOSI ports on the programmer. Is there not the potential to damage the programmer in this instance? The reference design shows these ports are direct back to the onboard MCU.
Also, if I am trying to program an ATMEGA328 that is already running code that is using D11,D12,D13 - does it not intefere with the programming process? (I am assume the ATMEGA is reset/disabled from running current code to allow burning to complete)?