I think you are understanding very well CKLD. You are not daft.
Intersex is a rather old and misleading term. This is a UK site for parents of children with Differences in Sexual Development which is helpful to read.
https://www.dsdfamilies.org/faq It is notable that medical intervention for children with these conditions is becoming more conservative.
DSD has nothing to do with the 'boys having periods' business. That is more to do with a political theory where we are 'reclassified' according to 'gender' ie how we present and identify rather than 'sex' which is whether we are male or female ie produce sperm or eggs - 'old fashioned' biology. Brighton is of course a leader in this field. If you want a headache, you can read about 'queer theory' but you do have to read around it fairly carefully as sources such as wiki are often re-edited by various factions.
The boys who will be having periods are likely to be girls who feel they are boys. If they are being treated by the GIDS clinic in london, they will be given GnRH inhibitors ('puberty blockers') which some on these boards may be familiar with as they shut down the reproductive system for a short while (prostrap) and then cross sex hormones which atrophy the female reproductive system. Therefore, their inclusion is political rather than practical.