No, do not buy the piston first as you do not know how far the machine shop will have to go to clean up the cylinder.
Just give the shop the sizes of the oversize pistons and they will stop at the smallest diameter that will clean the cylinder. Then buy the correct piston.
If Metra has a standard piston to cylinder wall clearance spec, give that to the machine shop. Otherwise the machinist will have to use his best judgement/experience in the matter.
FYI, the Honda Hobbit manual says that the stock clearance is:.050-.025mm max .150mm