Generally, the country code isn't needed for in-country calls, so I'm not surprised that it's omitted - you wouldn't use the +41 country code on most calls.
I'm not aware of any way to tell Safari to include the country code when autofilling phone number fields. I can see how it might be useful sometimes, especially in Europe where there's more cross-border interaction... just a question of how Safari can determine when to include vs. exclude it.
At the moment, the expectation is that the web site can add hints to the browser that any given field is a phone number, and can provide placeholder text to show the expected/preferred format, as well as validate the field entry is (or at least looks like) a phone number. However, there's still no guarantee that Safari will add an international prefix even if the field hints at wanting one. It's probably a larger web standards issue than Safari, per se.