Thank you for all the answers.
We got great deal on brand new Fuji Track Elite 2021 from Fuji Germany, 1200 Euro, so we will surely buy this frameset. It's only a matter of size. We will get 56 frame for testing and we'll see how my son feels and looks on it.
58 has 11mm more stack and 14mm more reach, so very little difference.
Unfortunately our national junior team doesn't have any bikes as resources that could be given to members of the team. So we have to buy the frame and crankset ourself. Whels are no problem, they have many of them including Campagnolo Ghibli from elite team if necessary.
Elite team has Cervelo frames but very old and 1 or 2 Argon Electron Pro.
National coach has 5 jobs and I'm not sure if he will be able to help us with the fitting. So far we used commercial fitting from the shop owned by famous pro Michal Kwiatkowski.
I will probably ask our top track riders what frames they ride, but might be difficult to find someone who has similar dimensions.