That's quite an unfortunate scenario. As i mentioned i poked around some in the source code where i did some changes and built my own version of the mod. If you don't switch the focus the vehicle being loaded is almost sure to phase through the ground though i had mixed results on this. I'm not read into the intricacies of KSP modding but it seems quite strange that there's no other function able to ensure the ground loads without having to switch focus, are these hidden by the engine?
A UI option to disable vessel switching would be nice as this would, at least, not be necessary when in the air or in space!
I'd message you directly as to not clutter up this thread, but sadly i haven't actually made 5 posts yet, despite this account being 7 years old.