You are absolutely correct that a 4.1 build will make it "easier" to reach goals especially with a street/strip build.
We have done 10 4.1 engine builds over the past year and can positively say it is much more responsive and pulls harder on the street with the massive amount of torque at low RPM and keeps pulling to high RPM.
I seriously doubt that the ones saying "stay with the 109" have any experience with a properly set up 4.1?
One of my production 4.1 builds can run 9.90's at 18 psi and a 70mm turbo with over 3000' altitude, which a make that ~ a 9.7 at sea level.
As far as 3.625" stroke on a 4.1, you will not see any significant performance increase until you reach the upper RPM range.
Since all 4.1 turbo pistons are a custom piece, the stroker pistons we use are about $200 more for the set, and you will spend a few hundred more $$$ in clearancing and mock-up costs.