I can't really advise you there. I've not tried the MSI B350's, but have heard good reviews of them. Similarly for the Asus B350 Prime Plus, Strix. I personally have a bit of an affinity with Asus, and have always rated their products. Really it's a matter of personal choice.
Regarding the over riding compatibility question, whether or not the ram is on the QVL means it's been tested to work with that specific mobo. Even though modules are on the QVL, they may still not work as you want. For both mobo's, and all B350 right now, it's the bios updates that will help most with compatibility. The QVL is a guide.
For me personally, I like to make the decision on hardware purchases based on a a few variables:
1. Cost
2. Aesthetics
3. Features
And not necessarily in that order
after that, all the mobo's perform roughly the same as each other.
So my advice would be to choose the one that looks the best (or fits in with your PC design), has the best features (RGB, Dual GPU etc) and that it fits in your budget.
Given your getting both - maybe try them, and see which one YOU like the most. Most of us here don't get the opportunity to pick between the two (we just review and make a decision that way). You have the benefit of trying out both.
I like that option, just from the point of being able to
Edit: BTW, OC the 1600x on those mobo's is quiet easy. PM if you think you might wanna go that route, and I can give you some quick settings for a simple moderate OC