Never a silly question, if you don't know the answer.
Which engine combo are you asking about? The 3900 and the F40? Welllllll... To tell you the truth, I don't have a clue as to why GM does anything that they do. Ever. Somewhere, it probably has to to with the $$$ - both for development/implementation and warranty concerns.
The 3900 was much simpler than the 3.6 DOHC (which is reputed to have timing chain issues) and only gave up about 12 HP, so there's that.
The F40 was because GM still cared that people wanted manual trannies. (No longer the case.)
The 6th gear was for fuel mileage considerations. If I were to go nuts and swap a manual into my G6, it would be a five speed. But fuel mileage is not at the top of my list.
Boost (turbos and blowers) is expensive to implement. Especially on "garden variety" cars, which ours are. Sorry, but it's true, no matter how much we love them. They replaced the Grand Am, after all.
There were no 3900 engines with either blowers or turbos in the pipeline, and weren't ever likely to be. Development costs bunches of $$$, and the ~60 degree separation between the cylinder banks doesn't leave much room for a blower, anyway.
(I understand the 3800 supercharged was killed for emissions reasons, BTW. So maybe blowers weren't the wave of the future, in GM's eyes.)
With that said, there is an engine that is an "evolution" of the LY7 - i.e. "our" 3.6 DOHC. It's called the LF3, and comes in some Cadillacs (See where I'm going with this?) It's a 3.6 DOHC twin turbo. Makes 420 HP. I know a guy who is swapping one into a Fiero as I type this. He's about 75% completed.
(I know another Fiero guy who has thousands of miles on an LS4 swap. It's a thing of beauty, and stone reliable.)
By the way... Fiero stuff is where I have gained most of my info from. Fiero people are certifiably insane. But there are some supremely talented people who play with them. I just try to watch, and learn all I can. The cool thing is... most of the technology is directly interchangeable with the G6, and most other FWD GM cars.
I can post links to the madness, if you'd like. I don't know if the mods would object, but they may. Regardless... there is a wealth of info out there.