Comparing the two is perfectly reasonable.
They are both dirt cheap fighters which throw 3 dice and have Swarm.
Hard to get much more comparable than that.
I think you misunderstand Zepnick's point - he's not saying that they're not comparable, but that comparing them on their own isn't going to produce the most useful conclusions. It's much more interesting to compare how they fit into each faction's play style.
The way I see it, there is no point in comparing the two in a vacuum.
Each faction offers diverse fighters that result in completely different types of synergies.
There will be Headhunters protected by X-wings and Jan, and there will be Tie Fighters buffed by Dengar and Howlrunner.
I think there's an interesting note there that the Rebels' squadron synergies boost the defensive capabilities of squadrons, where Imperial synergies boost their attack. It fits completely with the theme, but it also means that they need to be used differently on the board - buffed TIEs work better if thrown at the enemy to do as much damage as possible, where the supported Z-95s will be able to last longer whilst tying up enemy fighters.