Hmm, changes since HMv4.0....
Well, the 4.0 was a pretty good board, it had less noise on the probes than the 4.1, but....
The 4.0 was the last board that had the RCA jack for the blower output, from 4.1 and beyond the HM uses a CAT5 jack for the output. This CAT5 jack has the blower output and servo output wired to it by default, and you can use the 4 spare wires in the CAT5 wire for whatever you like, for instance, sending the probe output through the CAT5 jack as well. The 4.0 board does not have any header to connect a servo, however, you can connect a servo by jumpering a wire directly to a pin on the ATMEGA, +5v and gnd.
The HMv4.0 was the last board that pulsed the GND on the blower rather than the +12v, on the HMv.4.1 the blower drive circuit was changed to pulse the power instead (+12V), this way the servo and blower can now share a ground in the CAT5 cable. On HMv4.2 the blower drive circuit was updated again, this time to include a feedback circuit to the ATMega so the blower can run in the new VOLTAGE mode, rather than the standard pulse mode which creates more noise that can interfere with the probe readings.
Speaking of noise, in the HMv4.2 Bryan added an RC filter on each probe which GRATELY reduces the noise level on the probes. This not only makes the probes read more steadily, it makes the HM operate in a bit more relaxed fashion rather than hyper-correcting for noise spikes. Bryan actually re-routed the entire v4.2 board, for the first time keeping noisy power components away from temperature sensing component and paid attention to routing to keep sensor circuits isolated from power noise, these changes made the HMv4.2 the board with the least amount of noise picked up by the probes to date. On previous releases some probes had problems dropping off at room temps (though they work fine at grill temps), the clean running HMv4.2 will register probes down below freezing without an issue. This is nice if you do winter cooking, cause the HM will really flake out if the pit probe is dropping offline, which makes firing up the pit in the cold a PITA (I used to have to put the HM into manual blower mode until the pit heated up with older HM versions, that's all in the past with v4.2).
Finally, as you pointed out, the HMv4.2 mates with the rPi in a really low profile package, making the HMv4.2 fit into the smallest case yet for any HM. (least important difference if you ask me)
So, bottom line, I like the HMv4.0, it was a good board, the 4.1 was a bit rough (more noise), if you had a 4.1 I would say for sure you should update to 4.2... That said, I think the above improvements make moving from 4.0 to 4.2 worth it, the HMv4.2 is the best Heater Meter released to date.....
Keep in mind, parts wise the blower circuit is completely different, all the NPN transistors on the 4.0 have been changed to MOSFETS on the 4.2, so there are a lot of parts that are added/different on v4.2 compared to v4.0.....