Let $F$ be some function graph to graph which preserve graph isomorphism.
Example of such $F$ are the line graph, the $k$-subdivision of $G$ and many others.
$F$ need not preserve the order, the degree sequence, the girth, the size of the maximum independent set and others.
Q1 Must all $F$ preserve the order of the automorphism group?
According to my limited experiments, the answer is positive.
Added: In comments Brendan McKay suggested counterexample for the subdivision transformation and it is the cycle graph.
According to my experiments (modulo errors), subdividing a non-rigid graphs preserves the order of the automorphism group.
Q2 How to explain this observation?
Some tested subdivision examples from sagemath and the "nauty and traces" database:
PetersenGrap, PaleyGraph(73), SRG_100_44_18_20, "had-20" of order 80, "sts-21" of order 70.