For those with non-Latin alphabets that share letters, how do you avoid confusion?

In some alphabets, like Cyrillic, there are letters that look the same as Latin ones but have a completely different sound (for example, Cyrillic "P" pronounced as "R").

For people who use both systems regularly (or grew up around both), how do you avoid confusion? Do you switch mentally depending on the context, or does it become automatic over time?