We were exactly in your position!
We are the owners of a Swift 41 Fly, and also wanted a better Flybridge cover to make better use of the Flybridge area with an enclosed solution. The sun here in Australia makes an uncovered flybridge practically unusable. We ended up having a custom cover designed with a fixed stainless frame and supports with a Stamoid material cover. We also added clears to the solution as well as 4 x 360 Watt solar panels and Lithium house batteries. We also added a Euro awning for the flybridge rear.
The short answer to your question, in our expereince, is that there is no practical difference to stability etc. Note that with the generator fitted and the two engines, there is a fair amount of weight down low, so I was not expecting a large affect.
In windy docking conditions we roll up the Clear windows to reduce windage effect.
We are very happy with our results and have plenty of solar capacity plus a great protected flybridge area. We now only need to use the generator for the electric oven and heavy use appliances etc.
I hope this helps.