The whole assembly is something to keep the quartz at a given temperature. The foam also somewhat isolate it thermally.
@Dave: It's is not frequency programmable like the previous models, it's only trimmable by the rs232.
The 10 MHz output on the RS232 comes from the Xilinx CPLD and is a direct divided frequency from the onboard VCXO (60 MHz / 6). The square wave goes through a LC filter to that small RF connector and also to the DB9. The "odd looking" DB9 has actually a small filter in each pin that filters the signal even more.
The Analog programmable chip is used in the loop that drives the cell for fine adjust. (and that loop is used to regulate the control voltage on the VCXO).
Previous models had the DDS on the output, allowing for easy reprogramming, this is not the case on these new models.