Model-engineering drawings and any accompanying constructional articles very rarely if ever come with tolerances. They might become more common on items such as locomotive frame-plates bought laser-cut from a materials stockist whose system needs such tolerances. Otherwise there are no formal dimension controls in the hobby; just the principle of working to the best of our workshops and abilities.
If you are making something that does need a good-quality fit such as a piston and cylinder I can only suggest being guided by the industrial standard classes of fit summarised in publications like the Zeus books.
I don't quite follow the logic as you have phrased it though. I am guessing you are actually building a Weir-type pump. Your text seems to ask if the alignment is a function of the fit of piston within cylinder, but I am sure you do not mean that. A piston should be a smooth sliding fit for the full length of its stroke, and both it and its cylinder should be as closely cylindrical as possible.
If the machine has a rigid rod connecting two pistons in separate, in-line cylinders, the quality of alignment should be controlled by the surrounding metalwork and the concentricity of cylinders, pistons and rods; not by the fit of the pistons in the bores. As I am sure you realised, you cannot correct misalignment here by turning the piston down – that would not work at all.
The closeness of the bore to the drawing is of secondary importance to these, within reason measured in "thous", as long as the piston hugs the cylinder wall as it should.
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There are no tolerances for two reasons.
Firstly, we are not normally making interchangeable parts in the way vital to industry. It would not greatly matter if someone else making the same engine as you, machined his cylinder bores 0.005 " larger than yours as long you both made the pistons to suit your own engines. Yet obviously if you swapped the pistons with each other, that mis-match would give an engine kit that cannot be assembled, and one that can be assembled but would not run.
Secondly, model-engineering has always worked on the principle that as most of us are not professionally-trained machinist/ fitters or designers using full industrial facilities, we have to follow the drawings as closely as we can with the abilities and facilities we have, so we tend to make mating parts fit each other by specific example.
You do see some notes like "A must be a close sliding fit in B", or on some older drawings, the strange term "bare" after the dimension. Tolerances though; no. You bore the cylinder as closely as you can to the design, and turn the piston to a slightly firm, smooth and even, sliding fit.