This is not something canon-supported, of course, but it can just be possible that the time-travel device functions differently depending on some factors we don't know about. Maybe it returned Jay back to the physical state he was in because time-travel affects the person differently when the jump spans half a minute (like classical mechanics not being applicable for small objects). Maybe Jay has put in some settings into it to make it behave this way.
We only see it being used a couple of times besides this particular instance, why do we assume that this is how the device always works? I never really understood this attitude with all non-real tech in movies and books.
Out of the universe, there is no indication about how the device works because the film isn't centered on the time travel per se. In my opinion, you can't blame the director for not spending precious movie time to explain a small detail which doesn't affect the plot in a significant way. It's not really that important how Jay defeated Boris after all, it only matters that he did do that.