Yep, You're dead right, It does reduce the compression ratio. This is just one of the areas you pick up performance by blueprinting an engine. These mass produced engines aren't madeas thousands of special one-offs. To last 200,000 miles and not leak and run consistantly day in, day out, an engine doesn't need to be perfect . It just needs to seal properly, have good compression , and mechanical integrity (from a design point of view). To mass produce them cost efficiently, it doesn't matter if EVERY engine is perfect, as long as its within their tolerances and will make at least the baseline power requirement. To make EVERY engine of a particular model run accurate to the blueprints (rather than the tolerances) would cost in machining terms more than any gains they would achieve so they dont do it.
Exapmle: They have a run of castings come from the foundry. These castings deck height are running at 9.75" raw cast. To get a good seal area for the cylinder head the machinist only does 1 run and takes the block down to 9.625". Rather than follow the blueprints and re-run the block down to 9.5", he pushes that one along and sets up the next one. This means that for roughly the same amount of time he has done 2 blocks acceptable to tolerances instead of 1 block acceptable to the blueprints. That extra .125" wont worry compression to the point where ITS the reason the engine wont make acceptable power. Cams , heads and fuel type /ignition will make a lot bigger difference at this stage.
Also , yes you probably wouldnt get a .250" varience in modern engines but my example was a chevvy smallblock, a design running back to the'60s. This also is another reason why "blueprinting" USED to be a big power gaining method.
Hope I've helped you understand at least a bit better.