It's been a while, but I don't think alternate picking is left unmentioned for long in the course is it?

If you're already accomplished with it, I can't see any reason not to use it if you prefer to.

[br]The direct answer to your question though was apparent to me at the time, is for reasons of simplicity facilitative to easy quick accomplishment, like the lessons featuring 'simple' Am & Em.

Alternate picking won't lead to any "bad habits" I'm yet aware of. It's just that it's unnecessarily more difficult at that stage and thus impeding of perception of progress which is important commercially to GT given their target core demographic and objectives, and motivationally for the average beginning player and their own primary objectives in initial stages of learning to play guitar, whether cogent of them or not.