Even I was having the same doubt. The architecture, I guess, does change. Please anyone correct me if I am wrong!
I searched over net for transfer learning with different sizes and it led me to this blog post from Adrian Rosebrock which confirms the change in architecture.
I also came across this thread from the forum where Jeremy says that fastai automatically handles it and later in the same thread mentions about having used adaptive pooling to do so.
I am still new to course (and the techniques), digging through the excellent fastai library to find where and how exactly this is handled. Any pointers will be useful though!