How can I fix hollow cream puffs?
This recipe uses a substitution for a key structural ingredient (gluten), which is always likely to lead to compromises. If you omit the xanthan, it is even less likely to work, basically it has nothing to hold the structure. Some bakers are happy with the results of such substitutions, but for you the final structure seems to be quite important. 

The first thing you should do is to use the xanthan. If that doesn't help, there isn't much else you can do except try to be perfect in your temperature at every step (while still using the xanthan).