Many of the microbes used in sour beers and yogurt also play a role in our digestion. Members of the Lactic Acid Bacteria group (Lactobacillus, Pediococcus, etc) are prominent members of the bacterial species that make up our gut microbiome, in addition to hundreds of other genera. Saccharomyces and other yeasts play a role as well, although Brettanomyces are not considered a major influence.
Some people are quite sensitive to the addition of microbes to their gut, hence the stomach discomfort/gassy complaints, but this may be due to a personal (genetic) sensitivity. Your gut microbiome is actually pretty stable, although dysregulation of the proportions and presence of particular genera are implicated in many systemic health issues, such as obesity, IBD, and some neurologic conditions.
To acquire long-term health benefits associated with the probiotics found in sours, you must constantly "dose" yourself, which usually is not a problem, because sour beers are delicious. The constant introduction of these bacterial species will alter your gut bacterial flora, usually for the positive. Although, as you mentioned, the alcohol content limits the viability of some of these organisms, so in reality you are drinking very few viable cells. Once you stop, however, your gut microbe populations usually settle back to a "normal" state for you based on your diet, exposures, and general health.