Lets start with a definition of what internal geometry is. If you take the engine's stroke, which is the distance between top dead center and bottom dead center, (the distance the piston travels), and then locate the length of the connecting rod, you have the two numbers necessary to calculate the rod length to stroke ratio, which is really what we're talking about as "internal geometry".
If you divide the rod length by the stroke, you get the rod length to stroke ratio. On the H23, the rod length is 141.5mm and the stroke is 95mm, so 141.5/ 95 = 1.49 to 1. The 1.6A engines have a rod length of 137mm and a stroke of 90mm, so the ratio is 1.52 to 1.
These numbers are only effected by these two deminsions, and changing one or both is the only way to affect a change. Porting, head gasket thickness, piston configuration, and aftermarket rods(if they're the same length as stock) all have no affect on "geometry" at all. If you change the stroke or the rod length, you can change the "geometry".
Now, I'll assume that an explanation of what this "geometry" has to do with anything. Several things are directly effected by geometry, piston speed, piston acceleration and decelleration, piston dwell time at TDC and BDC, piston side loads, cylinder loading, and bearing loads. Almost everything mentioned as "effected" plays a major role in the way the engine breathes(piston speed, acc., dec.), the combustion characteristics(again piston speed, etc. and dwell time), and friction / wear characteristics(piston side loads, cylinder loads, and bearing loads).
There are many opinions on this subject, but it's generally felt that the lower the ratio numerically, the worse the geometry. As far as I'm concerned 1.75 to 1 is the ideal rod length to stroke ratio, regardless of application, and any number going down numerically is not favorable. If you lengthen the rod relative to the crank and the ratio grows larger, the wear goes down as does the piston speed, but this will contribute to an engine having a very narrow useful torque range. If the number is between 1.8 and 1.7, it's workable.
Since most Honda's have ratios that are on the low side, I'm sure that you're wondering why and how. The main reason that the rod length is "short" is because a short rod allows a short block and a more compact package to put under ever lower hoods. Honda uses a small bore and when coupled with a stroke that's not terribly long, the rod angle is still "severe" but not as bad as it'd be if the piston were larger in diameter. Honda also uses an excellent method for lubricating the engines, and engineering and material control is outstanding, which allows the performance and longetivity we expect.
These ratios and the resultant geometry is also the reason that so many Honda engines push pistons through cylinder walls when "boosted".
As I'm sure you see by now, books can be written on the pro's and con's, but I hope that you understand what we're referring to when you see Internal geometry. By the way the DelSol B16A2 engine has a stroke of 77mm and a rod length of 134mm = 1.74 to 1, and I assure you that this number didn't simply "happen" for no reason.