Flour is produced out of grain. Grain is kept in silos. And it takes lots of effort to keep the silos safe from pests and rodents.
So how is it considered vegan to eat food whose production requires dozens (hundreds?) of mice/rats to be killed (by fumigation and/or similar processes) in order to produce, let's say a, ton of flour?
Realistically, it is not possible to live in the modern world without being complicit in at least some harm of animals, including death. You've cited one example where, for an individual, it is difficult to avoid (i.e. use only flour-based products where this practice is surely not the case). There are many other examples, whether from medicine (animal testing), logistics (roadkill and railkill), or others (how many animals suffer due to anthropogenic climate change?).
Ultimately, it is up to each vegan to decide where to draw the line, which is a subjective question. I think most will draw the line such that they avoid direct animal products (meat, dairy, leather), but accept the inevitability of being complicit in indirect animal involuntary harm.
See also: Many plants need animals to grow (pollination, worms digging up the soil, etc.); when is it still vegan?, Are animal pollinated foods vegan friendly?
I'm not sure that saying that wheat production would require mice to be killed is entirely correct. A wheat farmer would not need rats to produce wheat. If they are present, it's a challenge that they have to deal with. This is why I prefer to stick to the dictionary definition of vegan, which is someone who avoids products where animals are intentionally used to make them. So that means things like meat, dairy, eggs, honey, leather, fur, etc. People who do that can call themselves vegans.
All the other considerations stem from the fact that vegans are conscious about the impact they have on animals and the environment, and everyone tries their best to go a step further to minimize their footprint on the world around us. I think the attitude should be to applaud positive changes but not expect, judge or compare vegans to see who goes the furthest. Because we have to remain practical, and making it too difficult to be a vegan might just deter some people from considering veganism, and continue to consume animal products which is more harmful to animals and the planet in the long run.
As humanity moves towards a plant based diet, we will live more in harmony with nature, and many of these issues will be naturally resolved. For example, animals stepping into human occupied areas looking for food, often comes from the fact that a lot of natural habitat for these animals has been destroyed, and animal agriculture is still the leading cause of that.
Incidentally, there are alternatives to traditional "pest control", for example as done by Humane Wildlife Solutions.
Addition: In my opinion, people who care about animals (vegan or not yet) would avoid buying a wheat brand if they knew that it involved the practices described in the question.
My suggestion would be that if someone knows farmers who resort to such measures, to get in touch with them and suggest more compassionate alternatives. They already made the right choice to be plant-based farmers, it would be nice to help them do it in an animal and environmentally friendly way, such as adopting organic farming.
