I don't remember the actual dialogue but the script for the episode says:
COOPER
Do you smell anything? Burned engine oil?
JACOBY
No. I smell engine oil in the park.
I'm with smokey that it's up to the viewer to decide, is not an accident that they decided to leave this matter ambiguous... But to me the answer is quite clear judging the evidences. BOB was not a brutal beast who killed without thinking, he wanted to remain in Leland, didn't want him to get caught. That's why he put the animal hair (from Ben's office) in Maddy, why he phoned Laura from Ben's office, why he laughed when he was informed Ben was arrested... He wanted Coop and co. to get another suspect and that's why he killed Leland and left the vessel when he was arrested. The scenario of BOB killing Jacques (a suspect) makes no sense to me judging his future actions and that's enough for me.
Something else, I think that the scorched engine oil smell doesn't only indicate BOB's presence, but BOB being furious or disturbed... In the traincar, in the traffic jam, when Maddy was killed, when Jacoby was attacked,...