Collectively, it seems like plausible reasoning for him to exit the vehicle. The dispatcher himself even said "let me know if he does anything else". TM ran, had a considering jump on him and was quickly out of sight. Zimmerman likely thought, at best he may get a glace at him bolting out of the back gate. Regardless, getting an idea if he was staying inside or exiting the complex, while obtaining an close by address would have been fairly beneficial to police.
Its unknown if he truly was able to see if Martin in fact went down the T, or straight down the cut thru and went onto RVC. Or perhaps he did see Martin cut down the T, and as he passed by and didn't see him, assumed he may have managed to then get back onto RVC.
I think once Zimmerman passed the T and peeked over to RVC and saw nothing, he was a bit surprised and unnerved based on him not wanting to give personal information to the dispatcher because he didn't know where Trayvon was.
Zimmerman had the mindset from the start that based on the break ins prior, Trayvon could have very well been a burglar. Perhaps a bold one, coming up to the truck and trying to spook him. However once he ran, that clearly came off as an admission of guilt. Most anyone viewing someone them deem suspicious, watching them run off would likely reinforce that notion.
Besides, the likelihood of a property thief actually fleeing then deciding to come back and confront the person is slim. I can't say the last time I recall that happening. I think GZ knew that as he left the truck, however once he completely lost sight of Martin he probably felt a little uneasy, and wondered if this was something other than a residential thief.