Then why use a 4 inch crank? You know you are air flow limited. And you gave up some rod/stroke ratio. Both are backwards.
You would make more power (the math is so easy to prove this I’m going to assume you know it) by a bunch, use less cam timing to do it if you used a 3.79 crank and a 6.250 rod.
You had to buy a crank right? You had to buy rods (or should have) right? So the only up charge is for pistons and I’m pretty sure a 4 inch stroke piston and a 6.250 rod will bolt right in. So really no need for a cushion piston is you don’t mind 1/16 inch piston rings.
So…6.123/4 is 1.5308. You better have a cylinder head with a HUGE cross section to feed it.
6.250/3.79 is 1.6491, which is a full point higher rod ratio. That’s pretty big. And it helps with small cross section intake ports.
Thats just one way geometry affects engine building. You can’t say it doesn’t matter. Unless it doesn’t matter to you for whatever reason. Still doesn’t mean it doesn’t matter.