First, please understand that in most localities LE and the M.E. are joined at the hip. Next, focus on the fact that either LE screwed up in a massive way when they did not find the bag in August or the meter man has more to him that just being lucky.
To get to the M.E's position of undetermined homicide, let's set aside any possibility that the meter man was somehow involved in a sinister way.
This leaves a skull with duct tape (allegedly) wrapped around it and a double bagged body and, allegedly, also some clothing. The integrity of the bags have been compromised and bones have been scattered across a wide area. Flesh and tissue seem not to be availaible -- but there might be some. An entomologist (bug guy) has been brought in to assess what the bugs around the area might be able to speak to. This is likely the bulk of site evidence available to the M.E.
However, outside of the site, LE is taking massive howitzer fire for not discovering the body in August.
Now, the M.E. comes up with homicide from an undetermined cause. Unless the M.E. was able to totally cancel out death by accident or death from misfortune, they cannot logically move to homicide without some evidence to support that finding (except as a guess). However, from what the M.E. has said, there does not seem to be any such evidence and toxicology reports seem not to yet be available.
My suspicion is that the M.E. simply tried to lay down some cover fire for LE's screw-up by issuing a finding of "undetermined homicide". My further suspicion is that on the witness stand, the M.E. will reveal that they used reduction (it was likely not this, it was likley not that) or fuzzy logic to back into their "undetermined homicide" position.
As regards what evidence at the scene might support the M.E's position, is it possible that they found a chloroform bottle in the area? Yes. Is it possible that the clothing was blood stained? Yes. Is it possible that there was a rope found around the neck? Yes. Is it possible that there was a blood stained knife in the area? Yes.
It's possible the M.E, has more evidence to support their position than they are revealing. However, if they had any such evidence, the best way to protect LE would be to reveal it. But that did not happen.
During cross-examination, my expectation is that the M.E. will watch a defense attorney slowly pick their bones clean. It's a price an expert pays for "guessing".