Yes, put it in the readme file and/or mod portal description.
And if people don't read it, it's their problem... I'm not going to bother the majority with an annoying popup.
Also, not reading it is not bad either... I played xcom as 12/13-year old when it came out, with poor english skills and without any manual (or forum, or chat, or internet)... and I still had tons of fun. You don't need to understand everything immediately to have fun.