I must not be understanding you. You get a greater working distance with 60mm or 65mm than with 100mm? Please explain.
No, you get less. So the flash is closer to the subject (shorter flash duration, easier to freeze motion) and the close the diffuser is to the subject the better the specular highlights. More often than not I'm holding on to whatever the critter is perched on with my left hand, and resting the lens on that same hand to keep the scene steady. Pick a point where I want the focus to start, twist my wrist to lay the area of acceptable focus where it needs to be, and press the shutter...
This is a European Blue Mason Bee emerging from its cocoon. Osmia Caerulescens, male.
Tech Specs: Canon 80D (F11, 1/250, ISO 100) + a Canon MP-E 65mm macro lens (Almost 3x) + a diffused MT-26EX RT (E-TTL metering with -1/3 FEC). This is a single, uncropped, frame taken hand held. In post I used Topaz Sharpen AI, Denoise AI, and Clarity in that order.
Emerging Blue Mason Bee XI by
John Kimbler, on Flickr
So the shorter the working distance the easier it is to shoot at 1x and higher with a flash. Can even shoot on windy days, and grabbing onto a flower is easier when it's windy cause the breeze will mask the vibration that I create when I grab onto it...
This female Sweat Bee is using her mandibles to strip pollen out of a Sourgrass anther.
Tech Specs: Canon 80D (F11, 1/250, ISO 100) + a Canon MP-E 65mm macro lens (around 2.5x) + a diffused MT-26EX-RT with a Kaiser adjustable flash shoe on the "A" head (the key), E-TTL metering, -1/3 FEC, second curtain sync). This is a single, uncropped, frame taken hand held. In post I used Topaz Sharpen AI, Denoise AI, and Clarity in that order.
Sweat Bee Foraging in a Sourgrass Flower II by
John Kimbler, on Flickr
Also easier to get a short focal length lens above 1x. If all you want to shoot is closeups and portraits then a 100mm lens will work. But if you want to push the limits of what you can do in macro with live, active, subjects then you need a shorter macro lens...