I have a 44mm EWG and I've used all of the setups you mention (MBC, 3 port EBCS, and Hybrid). The MBC will not flutter. The Hybrid setup usually will not flutter, but it depends how it is tuned. If it's tuned so that the MBC is doing all the work at WOT, then it won't flutter, but Hybrid systems are not always tuned like this.
A 3-port EBCS will always flutter. It can be tuned to be less noticeable, but it's always there. Depending on EWG spring(s) and tuning it can be very noticeable. For an EWG setup on stock turbo, a 38mm EWG will probably be the way to go. Going overly large on a smaller turbo isn't going to help anything. At worst it can make boost harder to control.