Github can not only help you see the activity of the students (who has been active? what have they done? etc..), but also engage with the students and actively encourage them when they get stuck (checking the issues of their team, their planned/done tasks, randomly looking at their code).
This may be a bit of a challenge with 100+ students, but if you get the TAs involved it can be easier.
In one course, we asked students (30 students) to host their code openly (e.g., on Github), and to document their ongoing tasks (e.g., Trello). In some cases, students would ask for our help, but otherwise I would regularly track their progress through Github/Trello, to make sure they have a work plan, and they prioritize the correct tasks.
In this course, each project was different, and it allowed us to encourage student teams to help other teams and reuse existing work/projects/libraries (as long as they give them credit). All the students can access other students' work. In some cases, they would submit PRs/Issues to other teams.
In another course, we used Slack, and each student team had a Slack channel/group. The students have added us to these groups, and it allowed us to be involved in their work. Whenever they needed help they would @mention my name. I would also try to keep track (as much as I could with 80 students) and help if I saw they were struggling somewhere.
You're right that Github usernames won't match automatically the verified identities at your institution (some students even prefer it this way), so I manually match and keep track of those.