Does flashing with stock rom conflict with country specific GSM regulation? I bought my phone from a telephony provider in my country... After rooting the phone, I noticed some folder or drivers were having the name of my country's telephony regulation council... 

Since I don't know why those drivers/folders were there I was wondering if I flash my phone with a stock rom from firmwarefile.com will make my phone not able to perform GSM operations anymore ...
Those files which you see are probably mandated to be there by your carrier. Not knowing what those files are for is not a good reason to try to get rid of them. They may have been there all along but you can see them now because your device is rooted and can show files which were earlier hidden. You can check with the carrier or OEM what those files are required for ; you are not going to get rid of them by flashing stock ROM , if they are meant to be there
It is a phone purchased in your country and flashing stock ROM from OEM or from a reputable trusted source will NOT harm the functionality of the phone in any way (as long as you flash the correct ROM and of your region), but the moot point is what is that you are going to achieve by doing that ?