Grounding issue
You often HAVE TO connect the boards solidly to the metal chassis for heat transfer. However, for RF reasons you often do not want the digital board sharing the same ground as the RF board! There is plenty of noise at all sorts of frequencies on the digital board, and if that gets to the RF board, it is nearly impossible to filter it all out adequately.
Each situation is unique, but as a general example...lets say there is a DAC on the digital board supplying a transmit IF signal. Right at the edge of that digital board you might put a filter to try to strip off the unwanted digital noise. Then you run a coax line from the digital board to the RF board where another filter of higher quality waits. The input filter on the RF board reflects most of the out-of-band digital noise back down the coax cable, and you now have a relatively clean IF signal to upconvert.