It does look like silica inclusions some of which do not do much to edge and some do. from the report it looks like you are not lucky on that. That is one of the things with natural hones. You never know what you get after next lapping as the inclusion can be just bellow the surface and will be revealed by use and lapping.
I would gouge those out that they would be bellow honing surface and use it as normal (I do belive there is somewhere report about Mr Iwasaki using simillarly adapted hone for his work). It does not take long and is effective. I would not even bother with filling it with glue unless honing will show me tha it is needed.