This is a "by design" issue with storyboards: Apple assumes that launch storyboards are handling everything (all orientations), as you cannot tweak the startup view controller at all.
To make it work, with builtin storyboards we created two views with variations, that agree with what they show, so when ios decides to change - nothing is changing visually.
There is a catch, though, as you do variations NOT on orientation but on size traits (compact vs regular), and from experimentation it seems that on iphone what is important is the height class: regular vs compact does the trick (portrait vs landscape).