Way back when, they removed the ability for the two to stack damage on the primary target, because getting +400 damage on a bonus-range AA made for really reliable and obnoxious poke.
Later they decided that they wanted the combo to work better together, but not be as obnoxious as before, so they instead of allowing the stacking damage to return, they just added an extra effect to RFC that was synergistic with Shiv.
Overall, this mostly hit their goals. The combo is strong, but each item still has it's own identity (some champs still build RFC first, like Jhin). However, I would agree that they overshot a little bit on the synergy part. The three-item spike (IE+Shiv+RFC) is slightly too strong, IMO. It contributes somewhat to ADC snowballing (i.e. the ADC who is behind, with only IE+Shiv, is kinda worthless in comparison to the one with all three). And the other 2-Zeal-item-combos are crowded out by Shiv+RFC.
I would consider reducing the Energize CDR (whatever you call it) on RFC slightly (like 15-20% instead of 25%), and putting that power into it's AS or proc damage. Increasing the proc damage would probably do more to disincentive the combo (since the damage is still overridden by Shiv's), but that may not be necessary. Figuring out those details is what play-testing is for, so *shrug*.