Yeah, I always wondred about this too. How does the WM Mace droid fit in Mace's starfighter? Curious, because I haven't gotten the droid yet but i have the starfighter. Also, how does vaders droid fit in vader's ship?
The answer to both of those questions is "they don't." Despite the instruction books for all the JSF repaints (and Jebus help me, I have all six ROTS-style JSF repaints so far) saying "most astromech droid figures can fit in droid socket", it's a complete and total lie. The post-R4-G9 astromechs using that sculpt don't fit at all due to the foot hoses (you can count R5-D4 and any sculpts using the VOTC R2-D2 body/feet out on that count as well), and the pre-R4-G9 figures don't fit because their legs and feet are too big.
Even if you do manage to get them in there by squishing and/or destroying the figure, they almost look like they've had enough and are about to commit droidicide due to the amount sticking out of the fighter vs. the amount sticking in it. I think I recall seeing someone somewhere online that had cut about half the astromech body and legs off to get one to fit correctly, but again, that was the "worst case scenario."
I honestly think that it's yet another case of Lucas saying, "Where does R2 go?" to one of the art dept's designs and them just sticking a droid on the JSFs with no real consideration as to the mechanics of it all. At least with the AOTC-era JSFs it was explained that the droids were hardwired into the ship's systems and they didn't have bodies to begin with, but looking at the film design for the ROTS-era ships, there really isn't much room for their full bodies to be there to begin with.
"Oh Aquaman, you can't marry a woman with no gills!"