What equation to compare protein isoforms in a Western Blot?
In my opinion you should use this formula:

$$ \frac{\text{log}_2(\text{Iso}_1/\text{Iso}_2)}{\text{log}_2(\text{GAPDH})} $$

This will normalize the relative fold differences between the isoforms with the loading control- GAPDH.

Since both numerator and denominator are log transformed they are in comparable domains unlike the formula-2 that you mention in your question. This is just a modified formula-2.