"Could it be possible to fine tune the capacitor to properly detect a different duration between the upload reset signal and the Serial Monitor duration?
Or are they the same length?"
Don't know, never tried something like that or looked at the signal.
You can install the cap in the Power Header pins after you get your program running.
Maybe add a toggle switch in series with it so you can leave it plugged in all the time and turn it off/on as needed.