I have never messed w/bacteria or fungi. Mainly because I am an Infectious Disease physician and I dabble in Microbiology all day. The thought of putting things like that into my food makes me shudder. HA! I just use root gel with the classic 45 degree cut and shave some of the stem skin off to promote rapid rooting.
I don't understand why that makes you shudder. There are already bacteria and fungi growing on, in, and around any plant you grow. Many of them have a symbiotic relationship with plants and are vital to the plants' growth. Mycorrhizae fungi has a symbiotic relationship with the majority of vascular plants, rhizobia bacteria fix nitrogen for legumes, etc. These help to fight off the pathogenic ones, a sterile medium is more dangerous than one colonized by the good fungi and bacteria.
I keep it simple when making clones. Cut the base at a ~20 degree angle, cut off most of the leaves and leave about 3-4 leaves, then snip about 40% of the tissue from the remaining leaves off. Stick them in potting mix and keep it consistently moist for the next couple weeks. No rooting hormones or humidity domes or anything, and I never have any problems getting them to root. If I had a commercial operation where shaving a week off the propagation time meant more $ then I might go with something more high tech, but it works just fine for me. Of course, some people just like to build things too.