Why do we not get v rank in all the levels and get all the trophies for 100%? It would screw up the game time but it is actually beating everything in the game which is what 100% is

Achievements are not components of the main game mode, and as such, are not factored in the percent completion of it. When you complete the game, the only collectible VVVVVV keeps track of is the number of shiny trinkets collected during the playthrough. Additionally, the unstable frame rate of VVVVVV, especially in the tower, creates a large disparity of comparison between real time and the in game timer between various machines (sometimes different runs on the same machine). The only perfect way to measure speedruns of VVVVVV is through the in game timer, because regardless of lag, it is frame accurate. It's only in the case of glitched Any% where real time is a somewhat reasonable measurement, since it can be completed so quickly that pc hardware is unlikely to give much of an advantage in most cases. Even in this case, the popularity of the category shows. Measuring in real time for a run that can take over 36 minutes to complete can introduce much greater gaps only due to measuring in real time, which would greatly undermine efforts of players on inferior hardware in comparison to a hypothetical competitor on a machine that runs the game quicker and very stably.

If the category were ever introduced, someone would have to run it, there'd have to be some method of applying game time for anyone to take it seriously, and it would probably be called "All Achievements". The nature of completing all achievements under a real time measurement would be relegated to a mostly casual affair, and is made clear by the complete nonexistence of recordings of people doing so. Creating categories that do not have any preexisting activity or immediate plans to do so doesn't make a lot of sense.