I always assumed that it was a combination of the water molecules in organic matter interacting with the field generated that would cause the molecules to excite at a certain frequency which combined with the electrical field also generated by the organic would be enough for the time machine to work with and form a stable portal to the desired time period.

The reason why humans went in with no clothing or matter was to keep the calculations as precise as possible. The last thing your time traveler wants is a numerical glitch occurring and them winding up with their clothing fused to their flesh or having their hand end up looking like a mangled mess of flesh and iron because they brought a gun with them.

For the T-800 it wasn't a liquid based lifeform so there were no molecules that could be generate the frequency needed and that the machines electrical field was so enormous that it would cause calculation errors with the time machine. Which is why it was covered in organic material to achieve the same results as the organic but also because the organic mater was also able to partially mask the electric field of the t-800 which would allow the time machine to work without a problem.

But again that's my assumption.