Z22SE piston hight difference


I've recently bought a mk4 Astra Bertone with a Z22SE engine. It was very cheap and I knew it needed a lot of love. With the car I got a spare engine block (used to be in the car, due to bad maintenance was seized).
We tore down both engines and they have different pistons and rods. The rods only look different, but they are the same length, size and all that. But the pistons are noticeably different.
One engine had pistons with slight grooves for the valves, while the other engine has pistons that are shorter and without the grooves.

Now... both the block and the head are back from the machine shop (the original head was absolutely horrible, we ended up buying two more, selected one of those two and it still was in a pretty messed up shape, machine shop charged £280 for the head alone). I got a set of new pistons (.50) over and they are of the shorter-grooveless category. So I think that no matter what it should be fine, but I can't help but wonder...what if I assemble this essentially brand new engine and instantly destroy the valves?
Why are there different internals in the same engine? Does it depend of where it was made, what year it was made or something completely different?
Please help - I can provide photos if they would be helpful, please let me know.
Thank you