You can, however, build a version of the bootloader that does the initial "LED Flash" on some pin other than D13, or omits it entirely.
You would download the repository into somewhere like .../hardware/arduino/bootloaders/optibootnew, and run a "make" there something like:
make ENV=arduino LED_START_FLASHES=0 atmega328
make ENV=arduino LED=PB1 atmega328
(Note that pin names for the optiboot build are Port/Bit based rather than Arduino pinnumber based.)
(The modifications to the optiboot source that allow this to be done from the build line, instead of requiring source modifications, are relatively "new", and not in the version of optiboot currently distributed with the arduino IDE.)