In Jedi Academy, Fett has access to the game's disruptor sniper rifle, which can shred beings at molecular level. The two reasons Jaden can survive these shots are 1) the enemies don't fully charge the shots and 2) Jaden us Force sensitive and occasionally triggers the Speed ability to dodge the incoming shot. If Boba has access to something like a flashbang and can distract Trunks long enough with it to fully power up the shot fired by the sniper gun (remember, Tien's Solar Flare works on super beings in DBZ), he COULD have a chance. That is the only way I can see Fett winning/surviving.
On the other hand, Trunks is probably faster as his normal self than Jaden is using Force Speed, so he could likely close in on Boba anyway and knock him out and/ or kill him.
In the Star Wars universe (or galaxy... hurr hurr), Boba can outrun his enemies simply because he has the jet pack and Jedi can't fly (amazing leaps notwithstanding). Trunks CAN fly and thus nullifies Fett's only chance at fighting this fight on his own terms.