When I bring my thermos to a coffee shop, brew the beverage in their own mixer before pouring it in my thermos. There is exactly no contact between their equipment and my container, beside the barista hands (which they should periodically wash anyway) and between the butt of the thermos and the table. Also most of them give the thermos a few rinses & wash with the soapy water jet thingy before pouring.

I'm assuming you are much more conscious about this issue than I am (that's fine btw, people have various levels of germophobia) , but practically my whole office block do this without any noticeable health epidemic.

Also standard coffee shops (the Starbucks kinds) always have industrial scale utensil washers that rinse boiling water/UV radiate the utensils. Assuming a government issue the appropriate law, the coffee shops will be able to ensure your container hygiene just fine.