Kyle- I don't think the MAF Transfer being off will affect your timing, unless the load scaling is off.
I would think the charge plates would have little to no effect on any of this.
The MAF Transfer is the single most important part of the tune. It is hard for a Mail order tuner, like Brenspeed, to get a MAF Transfer dialed in first try. If you paid for a tune from them, I would do some loging on the dyno and send them the info so they can make needed changes. That should make your A/F correct as well as the load scaling, so the timing would be correct.
The thing with timing is there are MANY factors that determine what timing the car will get or see. You can command X* in the tune, but there are factors that clip spark, such as down streem IAT temp.