Basic question about viewport tag

In this guide it says "we recommend designing prototype content at your target device’s native viewport width "

But what if I don’t know what the device width that 's going to be viewing the prototype is? Does that mean some users will see whitespace on one side and there’s nothing I can do?

Yep.

Normally in web development this isn’t an issue because sites can be built to be responsive and everything can flex to the size needed. This isn’t really possible in Axure so the end result is you’ll end up with either whitespace or scrolling.

It is possible to make widgets in Axure that adjust size, but to do this with everything in a prototype, while possible, isn’t really feasible for any moderately sized prototype.