Interesting question. I went to my copy of Youngson's "Slide Valves and Valve Gearing", 4Ed, 1932, which goes deep into the detail, and I'd expect a mention if this was significant. The book is aimed at sea-going marine engineers studying for a Board of Trade Certificate, and although mainly theory there's a good dollop of practical as well. The book covers all the engines likely to be found on a ship; compounds down to simple single cylinder donkey engines.
GMJN's issue isn't mentioned. The book goes into friction, lap, lead, travel, cut-off, con-rod obliquity, power, cushioning, steam distribution, consumption, setting and other consideration, but not that one.
My guess is the effect is insignificant compared with everything else going on and is compensated within normal valve settings as other posters say.
I think the main effect would be the loss of piston area rather than loss of energy volume due to the piston rod taking up space inside the cylinder, particularly as the latter is tiny when the stroke starts and only reaches a maximum after the steam has finished working on the rear piston face.
Assuming a 300mm diameter piston with a 50mm diameter rod, the available rear piston area would be reduced by about 11% compared with the front. Sounds like it's worth fixing except the cure doesn't achieve much. Balance is achieved at the expense of the other side of the piston, so overall power output stays the same. Power output might be reduced, because oomph is stolen from the best half the piston to balance the other.
The piston rod must cause another power reducing problem. Inside the cylinder it absorbs heat that would otherwise be converted into useful work. Then the rod slides out of the cylinder into the open air, where it cools down. The naughty old piston rod pumps energy out of the cylinder – waste – and only one side is effected.
But it's just one of many reasons steam engines are inefficient. A good full size steam locomotive is only about 5% efficient and for reasons of scale small engines are worse. A really good one might get 2½%, most model engines rather less. When 95% of the energy input to an engine is wasted, it pays to concentrate on big problems rather than small ones. I suggest the Stuart 10 piston being unbalanced isn't worth fixing because the improvement has no effect on efficiency, or a useful reduction of vibration.
Vibration is another interesting problem in reciprocating engines, and maybe GMJN's issue was tackled formally when the Victorians attempted to build the high-speed engines needed to generate electricity. I don't know.
Dynamos are efficient only when driven at high rpm, and gearing up ordinary steam engines wasted lots of power in an unreliable gearbox. Many builders attempted high-speed engines fast enough to drive Dynamos directly and they all vibrated badly because big reciprocating steam engines are almost impossible to balance due to masses of heavy metal being rapidly accelerated up and down. As vibration is related to the square of the speed, doubling rpm quadruples vibration.
Early power stations were an outright public nuisance: how bad can be judged by London County Council's power station. It caused enough vibration to derange Greenwich Observatory's mercury horizon over a mile away. Nearby houses had plates clattering in on the dining table, pictures falling, and walls cracking. The Law was soon changed to limit the vibration a power station could cause.
Much effort was put into reducing vibration and might well have addressed GMJN's concern, but research ended abruptly when steam turbines provided a better answer. But perhaps there's something in the engineering literature circa 1900 that answers the question properly. I'm joining the dots and could be wrong.
Dave