So let’s say that I did not have a great high school track career. If I go to a division 3 college my freshmen year and have a break out season and run times faster than most of the athletes at a division 1 school, can the D1 coach there recruit me and offer me a scholarship as well(and help me with admission to that school)?
They can. There is an entire section on the NCAA website about transferring and wait time.
Whether a coach will notice you is another matter.