@tdreid, that is a great discussion point, and important enough to get right.
IMO jQuery, SCSS and Gulp are all great examples of ‘power tools’ I would love to see new students to using.
To be clear - my comment is as much about ‘when’ to learn x subject as ‘what’ is worth spending your time on.
Bootstrap however is not a ‘power tool’, it is a ‘prefab home’. - a bunch of pieces that are pre built off-site that a someone assembles. This is a highly limited skill(?), and the experience(?) you gain is not teaching you to solve real world problems.
When you start to custom build even the smallest Bootstrap class you will certainly run into challenges. For example, replacing their grid system requires a comprehensive knowledge of media queries and floats. But what you learn solving ‘wireframing’ will give you much more control over responsively positioning all future custom content.
Likely, your first concept of a custom grid system would be as clunky as mine. But you are now touching on 'what works when, where, why"… and your next version will solve another problem/limitation, and the next, until you eventually have such a clear understanding that you can *gasp create something better than Bootstrap.