I have particular qualms with this in technical documentation. For example, I'll often be talking about a string or command and put it inside quotes to make clear what is part of the string or command. If that's at the end of the sentence, the rules dictate my period should go inside the quotes as well. I can never bring myself to obey that.
I can understand where you're coming from but I've never run into that issue because I never quote commands or keywords, instead I change the typeface. Still, I'm a huge fan of altering grammar in small, consistent ways for the sake of clarity (that's where style guides come in).
