The font size should not be of such relevance - otherwise handwritten math would be totally ambiguous. Parentheses take precedence - always. Thus here we first compute $a^3$ and then square the result (which happens to be the same as $a^6$).
By the way, the fact that $(a^m)^n$ can be expressed simply as $a^{mn}$, whereas $a^{(m^n)}$ does not allow any similar rewriting, is the reason why we have the convention that nested exponentiation without parentheses is to be evaluated from right to left (or from top to bottom if you wish), i.e., $a^{m^n}:=a^{(m^n)}$.