Wrong, MDT =/= MAB/MDB.
Magic Defense Bonus only applies to MAB calculations, SWI / Atonement do not use MAB and this MDB has to effect. Magic Damage Take, aka MDT is a percentage reduction (or enhancement for some) on all magic damage taken. Magic Shield is 100% resistance to all magic type effects, both damage and status effects.
SWI / Atonement both are effected by MDT and Magic Shield, PDT and Physical Shield have no effect on them. Req isn't effected by Magic Shield nor MDT, it's not magic damage. It even stacks with Sneak Attack, the universally accepted litmus test for Physical vs Magical based WS.
On the test server I used Req on a PLD mob that had 2hr'd, it did 0 damage. Please feel free to test it again on a Invincible'd monster. Or go one step further, fight a Hydra NM, there are plenty in Abyssea, and wait for it to use Pyric / Polar Bulwark. Under Polar Bulwark it's immune to magic damage, so use Req and see if it does 0 damage. Under Pyric Bulwark (immune to physical damage) do the same. Based on it doing 0 to a PLD under Invincible, I'm fairly confident that it'll do 0 to the Hydra under Pyric Bulwark and regular damage under Polar Bulwark.
Now on that note.
Is there something wrong with your brain? I'm really getting tired of people trying to compare a physical WS to SWI / Atonement, both of which are magical WS. Just because there has never been a physical WS without a damage type set to Piercing / Slashing / Blunt you think it must therefor be magical. That is illogical, its a four hit (five with DW) attack with an -20% attack penalty. You can NEVER *miss* a magic WS but you can miss hits on Req. It use's the standard physical WS damage formula. The only thing different from this and vorpal is that vorpal is slashing damage and Req is non-specific, aka *non-elemental* in SE speak. Meaning it will ignore any monster specific damage resistances.