You can very easily attach a filter to the Canon 100 mm macro lens. First, attach the filter to the lens. Then attach a Canon Macrolite 58c adapter ring to the front of the filter. Finally, attach the Canon macro flash attachment ring to the 58c unit.
Thus, there is no need to attach the filter to the macro flash adapter. It seems to me that if the filter is thereby inside the tunnel formed by the flash adapter ring, perhaps it is less prone to be a source of flare light.
Lord V is of course right - for the very best possible image quality one should avoid filters unless of course they play an active role in achieving better overall photographic quality.
For myself, who needs to protect my lenses from my own clumsiness and accidents, perhaps a very high quality filter (thin, low reflectance) is an appropriate compromise. I've not been able to find any significant image quality loss if I use high-quality multi-coated filters such as the Hoya Pro1 Digital filters I mostly use. YMMV.
I haven't tried a lens hood fpr macro photography although I bought the one Canon sells for my MPE-65. Perhaps it would help reduce flare light in the complex mulit-element lenses we all use nowadays, as it does for non-macro photography. Keep in mind that digital photography uses sensors that are much more reflective than film, and there is the potential for the sensor to reflect light back into the lens for additional flare-causing reflections. Some of the newer lenses take this into account, supposedly.
My personal experience is that most photographic filters have excessively high reflectance, and are made of unnecessarily thick glass. As a result, they may cause unnecessarily high flare light levels, especially in unfavorable lighting conditions and if a light source is off-axis.
I have had success with Hoya Pro 1 Digital filters, probably because their glass is thin and it is multi-coated with very low reflectance. Many other filters, including some brand names, have high reflectance and I don't see how such characteristics could be good for photographs. One has to be extra careful to keep multi-coated (low-reflectance) filters clean since even a small amount of dirt or smudges will greatly change the reflectance of such filters at the dirty location(s), increasing flare light, etc. I find that a very mild dish soap plus running warm water works great as a cleaning method. Just be sure and avoid rubbing sand or dirt into the coated filter glass - gently rinsing it with soapy water has worked well for me.
I hope this info and my comments are helpful. I don't claim that I have significant information or experience but am merely trying to share what I have acquired.