Minimum quench distance on a high performance automotive gas engine is 35 to 40 thou. Factory tolerance is usually between 60 and 100 thou., but with stricter emissions and higher compression ratios this number is closer to the 35 number.
These little diesels run much tighter than that because of the limited rpm they see and the small bore. Personally I would go no tighter than 20 thou.
You can absolutely have the pistons tops milled, if you determine you do not have enough clearance. It's done all the time. It is up to you to take the proper measurements though, and use the compressed thickness of your head gasket for your calculations.
If it's strictly for the prechamber interference, you can clearance the piston with a dremel and a steady hand. You're only taking the equivalent of the amount of head milling that was done, which is easily achieved.
As to the question about the rod reconditioning changing the piston height, If the job is done correctly the center to center dimension of the rod does not change. Therefor the quench distance should remain the same.