I think this lines (#52-54) in the gdm.transform function introduce an error in the result:

if (geo) {
   predInd <- c(1, 2, predInd[-1] + 1)
}

The error appear when geo = TRUE but geographic distance has all values in the i-spline equal to zero. Then, predInd doesn't include the geographic term and removing the first element remove one of the environmental variables from the output. I guess a potential solution is to check whether geographic distance knots has all zero value and then not to remove the first element from predInd.

      if (geo) {
        if(sum(model$coefficients[1:model$splines[1]]) == 0){
          predInd <- c(1, 2, predInd + 1)
        } else {
          predInd <- c(1, 2, predInd[-1] + 1)
        }
      }