I tried to use a commercial beer bottle that looks exactly the same as my homebrew bottles, picture related: 
But when I tried to cap with a Red Baron capper, this only pops...
The opening of the bottle looks pretty similar, and the caps are the same size... Why is this not working?
Topic commercial bottling homebrew
Category Mac
Since you have the red baron capper, the crown size is actually interchangeable. Noted in the below picture, these metal brackets on each side slide out, revealing a different size crown on it's opposite side. You can then flip the bracket and slide it back in.
This is where I would start, especially since you state the caps are the exact same size. I have encountered commercial bottles which have the common mid-size caps, but require the crown setting on the capper to be set to the larger size.
Some bottles have different size lips, and some cappers have different size crowns. While they look the same they are going to be just slightly different. What you try to cap the bottle, the neck will shatter.
26mm is the midsize cap, which is common throughout the world, but there are larger 29mm size cap, which is used in Europe (common on Belgian beers) and on champagne bottles. Some breweries in the US are also starting to use the 29mm caps.
I have not found an outlet for 29mm caps, but I also didnt look that hard. When I found out my capping crown was 26mm (which you will get from a homebrew shop) I just started only collecting those 26mm bottles.
Hope that helps!
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