should I care if the pronto hex is in RC5 protocol or NE protocol for example or I can just transmit it as is?
you can in principle transmit them "as is". However, decoding them has a few advantages_
1. Many of the signals you find at this site, or learn yourself, are "dirty": The measured durations are slightly off, in some cases a capure even contains multiple copies of the real signal. Using "dirty" signals decreases reliability and range.
2. A decoded signal (more precisely, the parameters) take up much less space than a number of durations. Important if you have little memory and many signals.
3. You have a better "understanding" if you have the decodes, for example if you decide to go hunting for not documented commands.
