I believe the shell bonuses over ride the armor bonuses. You definitely don't get both. I also already had a complete BM Weaponmaster set and had to go back and purchase BM Vindicator once I learned of this route a few months back. It took me like two nights playing roughly 3 hours to grab the needed Vindicator pieces. While you technically wasted comms grabbing Weaponmaster first, you are also fully geared in BM making it easier for you now to do well and earn comms faster. So it won't take you long to get four BM Vindicator pieces.
REMEMBER... You only need 4 BM Vindicator pieces to trade in on 4 WH Vindicator pieces. Don't buy the chest, it's the most expensive and the stats are the same on the WH Vindicator and Weaponmaster chest components. You'll be changing the mod and enhancement in the long run anyway, and like I said, the stats on the armoring are the same.
So just trade your BM Weaponmaster chest in for a WH Weaponmaster chest. And then go back and purchase head, gloves, pants, boots of the BM Vindicator set and trade those in on WH Vindicator items. And those four Vindictor pieces will give you the four piece set bonus you need.
It's worth the time. My highest dmg game was 375k and on my first match with this set bonus I hit 495k with a great healer and have averaged 350k without a single healer on my team. If you can get a good 5 second rotation down right after force leap you can almost entirely melt any class except for a really well geared tank or a healer spamming heals. But in those cases, you're still helping your team because if your keeping their healer focused on themself then they aren't healing the folks your teammates are fighting!