This is a good WI, though the changes are less immediately earth-shattering than you may have assumed. All in all a shipping revolution is started, but it will take time to propagate.
To directly answer your questions:
...but this will give Italy the advantge it needs to became decent power in 1939?
To be honest, no. This alone will not do it by 1939. Still far too much corruption and inefficiency to overcome. It might, with some financial butterflies, boost the industry and economy some, but better shipping still won't make trucks come off the line any faster. Eventually the containers will allow for more industrial expansion and financial changes, but it will take more than 12 years.
What about the impact on geopolitics if Italy became a mayor commercial power?
Well, you'd need more than just shipping improvements to become a "major commercial power". You'd need to improve the inefficient bureaucracy (which Fascist corporativism just made that much worse). You'd need some sort of real export markets, which save for some trade in vehicles and weapons Italy does not have at this time. And again, this alone doesn't allow you to build any more vehicles to export in the short term.
Surely it will spring an industrial revolution of sort, but it will be enough to better itlian performnce?
Immediate Revolution? No. Eventual Revolution, yes, but it'll take time to propagate. For the short term: potential improved shipping speed, but there are still so many economic/industrial deficiencies to overcome. The shipping may start the ball rolling in that regard, but you're still likely decades out before you see major changes from the "modular butterflies".
You improve the potential turnaround times in port, but only if the ports are efficiently run. Italy at the time had very poor port authority management. Ships would sit at anchor for days waiting to unload goods even when there were spots available simply because the harbor master didn't get word they were there or that spots were open. Now, assuming someone with a penchant for organization like Balbo takes notice... A little Castor oil at the right place can really get things moving.
What will be the impact of containers (MODULI, metallic stakable boxes, ITTL) on Barbarossa?
Probably not too much. Bigger impact on North Africa since shipping containers really make a bigger difference at seaports where there's so much more cargo per single vehicle. They'll allow quicker shifting of materials in rail yards, which will help some, but unloading and distributing goods from a container isn't that big of a difference from unloading them from a box car. No Axis truck at this point is likely to be able to haul a shipping container across the inadequate roads of Eastern Europe. You'll need to move crates into trucks or unload by hand no matter what.
What will be the impact of containers over european infrastructure?
As stated before this is an idea everyone else will eventually steal. Eventually every port in Europe and America and finally the world will be equipped with container cranes. Eventually (post war) major highways in the autobahn mold will see shipping containers on trucks, but the container tech alone doesn't automatically spur highway building. Probably through the war years it'll be containers unloaded from ships onto existing rail or barge networks for distribution to regional rail stations and canal ports, then hand- or forklift-load onto trucks for local distribution.
The eventual changes will be drastic and this will spur globalization that much earlier, but a 1927 POD isn't enough time for the eventual impact to make itself felt for WW2 (assuming it's on OTL schedule).