Has the core firmware changed to allow us to flash new code over serial when the device is in “LISTEN” (flashing BLUE) mode. I previously had to put the device in DFU mode (YELLOW) to flash my code locally onto the device? Is this a function of my CLI tools, the base firmware on the photon, or both?
Both works.
You just need to use the respective switch
particle flash --usb for DFU Mode
particle flash --serial for Listening Mode
That’s been the case since the Spark Core 
--serial uses Y-Modem and --USB dfu_util
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