Good news! If I build using the Arduino IDE 1.0.6, then I no longer need to use a DTR-to-GND connection on my Moteino R4 when it's utilizing flash memory and when powered by battery-only (no FTDI).
So, although this started out as a thread on clone use of flash memory, the information gained is turning out to be highly beneficial in my use of Moteino R4's.
By the way, the R4 continues to be my preferred wireless platform.
[Edit: I do, however, still need the megaohm pulldown resistor on D12 if I am to wake-up the flash memory after explicitly putting the flash memory to sleep. Without the pulldown, even if the R4 firmware is built using IDE 1.0.6, the result is still in a hang when trying to wake the flash memory.
The unit I tested is an R4 running direct from two AA batteries and with the stock LDO voltage regulator removed.]