LE thinks (or, more properly, believed at one point) she was in his trunk when he exited the garage. That's based on the wording in their affidavits. But it's unknown as to exactly how they based that conclusion at the time.
There could certainly be much evidence we don't know, that forces the outline of events in one direction or another. We don't know what we don't know. Personally I do believe there was indeed a major struggle. But I do think that any combo of in/out of trunk at outset, and fight at/not at garage, is definitely possible. There is time, and there are plenty of ways, for any combo to have happened, and the events of that night didn't necessarily happen in the most likely way, but only in some possible way. Time up front is plenteous because he was much bigger, and we have to consider he possibly had the aid of some drug or gas or weapon to subdue her rather quickly. Also, he had the ability to know where she was headed, and act in anticipation, which was to her car.
For example, say he opens his trunk and says "Hey, come look at this" and then bonks her or sprays her or chloroforms her or whatever - that would take mere seconds. Or say he tries to grab her, she hits and bites, and THEN he knocks her out. The ending could be quick, so the setup could have taken a few in which he took some damage. Or maybe he thinks she is KO'd, then as he is stuffing her in his trunk, she bites and scratches and claws and he has to re-subdue her. Alternately, I could see her being subdued at the outset, stuffed in the trunk, but then The Fight happening when he stopped somewhere and she tried to escape.
My analysis? IMO it doesn't matter exactly when (to the minute) she was forced or placed in his trunk, but only that they prove she was IN HIS TRUNK (which, of course, is the crime of abduction). And the fact she was never seen or heard from again, to me that's a huge fact too that needs to be hammered home, since IN HIS TRUNK was the last place she was ever known to be. She was not there without his knowledge, and she didn't leave there without him knowing how/why/when/where - all of which speaks to the appropriate severity of punishment for him, since she's not been seen since. My punishment that fits the crime, is that he doesn't deserve any chance to roam the streets as long as she isn't home and able to do the same.