I will be purchasing an Atmega 328 to run a 3.3V as the Sparkfun version of Arduino Pro Mini. However, I am designing my own schematic which integrate other components and sensors...
I want to know if using these modules I will be able to burn the bootloader for the Atmega328:
The surface mount chip comes with a bootloader. Why do you need to burn a new one?
I think you are talking about the Pro Mini, I think the original poster meant they are building their own Pro Mini alike, and thus buying raw TQFP 328's ?? If one buys a 328p TQFP from a supplier it won't have any bootloader burnt on it by default.
Some people have been known to 'chop the head off' a 'Stripduino' ( tinkeract.com ) and tack that on their project board.
It has the bootloader burned in anyway but also has the 2x3 connector.
Just an idea.