I'd be happier if I understood how the changes in the schematic (a pull-down resistor on the other side of autoreset cap) end up causing/allowing this spike... (I also don't understand the motivation for ADDING that resistor in the first place,
so ... I dunno.)
PD7 is involved in high-voltage parallel programming; it's (renamed PAGEL) supposed to be tied to 0 to enter HV programming mode (which is somewhat backward from the observed behavior. But it certainly seems reasonable that HV excursions on RESET could trigger SOMETHING.)
None of the HV programming shields I've seen involve using that programming while the chip is mounted IN the arduino; they all move it to a separate socket. HCV programming involves 9+ pins, including the crystal pins, so it's not really meant to work with the AVR "in circuit."