I did a quick search here and on Reddit, and this discussion has occurred a number of times. None of discussions I looked at came to any definitive conclusion. Unfortunately the details of what is going on are not described on SWGOH.GG, so there's not really any good way to know for sure besides asking the developers. Are they doing one of those Q&A's anytime soon again?
Personally, I see no reason why an equalization effect would add or remove HP from the total gained or lost based on who you attack. Then it's also doing damage and not just equalizing.
Either way, attacking a weaker enemy is absolutely more effective. You do more damage against units with lower defense.