Now it makes ~1.8 CZK for small brewerys and double for big ones. (Per 1l of 11° beer)

In reality it levels the production costs in small scale brewing. The big brewerys still have the advantage of scale so they can lower margins.

The beer from craft brewerys is cheapest in pubs because it is much cheaper for small producers to get it to consumers that way, bottling process is on small scale too expensive.

On the other hand shops pressure big producers to make bottles and cans dirt cheap around 10 CZK/0.5l. They have to make it up somewhere so mark-up in kegs is higher.

This means that in pubs you can get good beer from small/local pub brewery at same price point as from big commercial brewery.

Edit: I had to look up the tax and it is double counted per 0.5l not 1l