Hi jarlington, and Welcome!

You ask some very good questions!

A couple of things: first of all, this is perfect: "Currently, I focus on two chords at a time during practice and use a metronome to build timing and consistency."

That is exactly how you want to go about it.

Plan to spend some of every practice session just working on that. Stick to chords that are likely to show up in songs you want to learn to play - and you'll get more enjoyment out of the work you put in. There is no need to master, say, transitioning to F#m (which is not easy) until it crosses your path within a song you've got your heart set on learning. Or, if you have moved on to studying barre chords.

Keep moving forward with the curriculum, AND, spend some time continuing to perfect your seamless chord changes. They are not necessarily going to get better "naturally over time". There are specific strategies you want to learn and bake into your physical memory. 

But you also want to HAVE FUN and keep learning new things, right?

So my advice is: do both!

Hope this makes sense and helps! 

Be well! - Lisa