Note that you can significantly alter your gut microbiome simply by changes to your diet.
Right now the link between the microbiome and allergies is tenuous at best.
Whether it makes a difference really depends on the individual. Personally I think it's better to get the gut bacteria that you can from your mother near the time of birth, but that's me.
I’m certainly not arguing there is no impact of the microbiome on disease, but right now the data is far to early to say anything conclusively.
The article seems to say the answer is yes:
...scientists think that the initial exposure to bacteria at the moment of birth could be a “thermostat” moment for the immune system, defining its sensitivity and which strains of bacteria trigger a response.