I don't think you should always use ISO 100. Just realize that high ISOs make for noisy images. There are definitely times when it is preferable to have a sharp, but noisy image vs a blurry image with little noise.
I do believe strongly that it is counterproductive to set your camera to some type of automatic mode and then pay no more attention to the exposure settings the camera is choosing. On the other hand, I am not one of those that think that anything other than manual mode is bad.
Just pay attention to what your camera is doing, and be ready to step in and make changes when necessary. Macro photography is one of those genres that, I believe, require a more hands on approach to settings.
If the Macro mode on your camera works best for you right now, then that is probably the technique you should use at this time. Just be open to trying other things and have an attitude of growth, vs stagnation.
As to what high ISOs do to an image, I went out and took two pics with my D3400 and the 18-55 lens. Both were cropped to emphasize the differences. There is a difference of sharpness in some areas, like the center, that is due to a different focus point, or possibly motion blur (it was windy. I was looking just to show noise, so didn't bother to set up to get two aboslutely identical photos.
This is ISO 100
This one is ISO 3200.
If you look at the first, it is smooth and has lots of detail. The ISO 3200 has a lot of noise , which is particularly evident in the green portions between the petals at the corners of the image. This also translates to a loss of detail. The higher you go, the more noise is present.
I routinely shoot at somewhat higher ISOs. This is usually when I am shooting with a long telephoto handheld, and often have moving subjects, like birds. In this situation, it is either a noisy image that is sharp, or a blurry image. The latter is unacceptable. The difference with macro photography is that, usually you are going to be using smaller apertures, for increased DOF, which means that you are going to have to either add light, or use a tripod which will allow low shutter speeds. If you are going to do that, then often you have the option of keeping your ISOs low as well. Also, with macro, fine detail is a very important aspect of the image, and should not be discarded needlessly.
If you need higher ISOs to get a sharp photo, then by all means use a high ISO. That is preferable to either not getting the shot, or getting a useless, blurry shot. FYI there is software that will clean up noise from high ISOs, although usually at a cost of detail, and noisy images already have less detail to start with.
The photos you posted that had ISO 3200, also had shutter speeds of 1/400 sec and 1/1600 sec. You should be able get sharp photos handheld with a 55mm focal length using VR at 1/20 sec or lower. The rule of thumb without VR is 1/focal length. IE at focal length of 55 you should be able to get sharp handhelds at 1/55 sec.