A shuttle shrugging off damage from a Negh'Var cruiser, or an Intrepid class ship shrugging off damage from multiple Borg Cubes strikes me as "magic" even if minor damage was done after enough shooting.
Why? It's exactly the same way that most modern Trek shows always treated shielding and battle damage -- each successive hit reduces shield strength to a lower percentage, much like in a computer game. They may have said this armor was more powerful and invented a silly-looking visual effect to represent it, but functionally its only difference from normal shielding was a matter of degree.
If your shields are knocked down to 40% less than a minute into a battle, that means you'd be dead in less than two minutes. That's pretty damn far from "magic" or invulnerability.
Then again the Borg had already been sufficently watered down as a threat in Dark Frontier and Unimatrix Zero, but not to the point of shrugging off all damage and blowing up Borg cubes with single shots.
There's nothing about it that's inconsistent with how we've always seen the Borg portrayed. Look at the very first time we saw Borg drones in "Q Who." The first drone was easily taken down by phaser fire; the second was invulnerable to it because the Borg had assessed the weapon and adapted to it. That's what the Borg do. They never
start out invulnerable; they don't need to, since they don't care enough about individual drones or ships to have a problem with sacrificing them. They just let themselves be shot or blown up until they figure out how to adapt, and
then they become immune to that particular weapon.
In this case, the weapons in question were from decades in the future, so the Borg hadn't seen them before and thus wouldn't have adapted to them. So
of course they were effective against the Borg
at first. But as is always the case, the Borg would eventually adapt and the advantage would be rendered useless. This was a major plot point in the
Destiny trilogy; Starfleet restricted the use of the transphasic torpedoes because they knew it was only a matter of time before the Borg would adapt to them and render them as useless as any other weapon.
So no -- no "magic," no "god mode." Just a temporary leg up against the Borg, a couple of weapons from the future that they hadn't adapted to
yet but inevitably would sooner or later.