Courses and course formats

I'm not sure I follow your categories but your cohort plan looks reasonable. When I look at Moodle, there are categories (where courses live), courses (where you put your content) and activities (the actual content, which may include Lessons, a type of activity). So, for me, it might be Category 1: Introductory courses for all staff (sexual harassment, legal stuff, it security, etc), Category 2: topics for Department 1, Category 3: topics for Department 2, etc (or alternatively, if Department 2 and 1 jobs overlap for some courses, maybe a category for like-topics). Then you go to the courses and enroll each cohort in the courses that apply to that particular group...cohort 1 in all the cat 1 courses, cohort 2 in all the cat 2 courses etc. I'd probably be more descriptive in my cohort names, numbering tends to result in confusion (but your numbering might be for example only). Does that make sense?

Or as examples:
Intro to Company (enroll Cohort 1)
How Not to Be a Jerk at Work (enroll Cohort 1)
Being Safe on the Internet (enroll Cohort 1)
Intro to Department 1 (enroll cohort 2)
Intro to Department 2 (enroll Cohort 3
Doing Job A in Department 1 (enroll Cohort 2a)
Advanced topics in JA D1 (enroll Cohort 2a)...etc...