Well, for me at least, the DIP version allows you to keep the board in case you fry the processor. I'm not good at soldering, and processors do go bad once in a while. In terms of investment and considering most people are not great with soldering SMDs, this is quite logical. Also, in case you want to use the board for a standalone project, you may use a (not so much) cheaper chip (ATmega32, 16, 644p). So for tinkering and prototyping, nothing beats the DIP version.
Didn't the first design use the surface mount ATmega1248p? :\
Also, why not use an RTC with integrated crystal? Something like this... Mixed-signal and digital signal processing ICs | Analog Devices
Last but not least, are you taking orders?