In my opinion, not only does a big man do well with high per in a flex, the big man with perimeter thrives. And it's not just three pointers. The flex is a constantly moving offense with so many cutters and the players are supposed to be easily interchangeable. If your 4 or 5 can hit an open jumper, it makes the offense much more difficult to defend. That said, the flex offense has a lot of variations that you cannot change in HD that coaches do in real life (ie getting your bigs closer to the basket for easier looks, compressing/stretching based on your team's strengths, etc) As far as HD goes, as I said earlier, I do think that bigs with perim help the flex offense greatly.
Since you're playing D3, it's a lot harder to get perim without sacrificing some athleticism/speed/defense, but it's still possible. Even though I don't think there's THAT much difference between the three main offenses (triangle/motion/flex), I still think the motion is the best for D3, but the flex certainly has its benefits if you can recruit for it.
Feel free to sitemail me if you want to chat about it more or have more specific questions