How can I encourage my advisor to adopt better work practices?
Turn the tables.  For your next paper, you maintain the master copy.  Make sure all the infrastructure is in place, including a fairly solid draft of the paper, before you involve your advisor in the writing process at all.  Use whatever version control and reference system you find most useful.

Your advisor may simply refuse to use your tools; fine, you can still incorporate their emailed inputs.  Or they may just need someone else to figure out the infrastructure and teach them how to use the tools, instead of figuring it out themselves from the manuals.  Either way, you'll have some extra work to bring your inexperienced (and possibly resistant) coauthor up to speed, but that's a standard part of the student-advisor relationship.

In the worst case, your advisor may simply refuse to give up control of the master copy.  (Never mind that it's already too late.)  In that case, you may need to encourage them to look for another student.