Well. . . .
I don’t remember the utilities auto expanding, but I do remember that there is a boot-time parameter that causes image expansion at boot time.
Seriously, I’ve been away from this for a while so the brain cells may need a “CAS refresh” cycle. 
Sounds like you have it all squared away nicely!
I hope you stick around and share more of your adventures with us.
I don’t know if this is relevant to what you are doing, but I get the impression that you are using both a Windows host system and a robot remote system to do your development and ROS research.
Background:
My most recent “serious” project is my respin of the existing “Remote Camera Robot” code where I had the, (ahem!), “brilliant” idea of replacing the clumsy mouse-based control with an actual joystick/gamepad.
This simple (!!!) idea turned into a major development project where I learned a lot about web servers, clients, Nginx, secure sockets, etc., and it’s still not actually code-complete, (IMHO).
In order to manage the code, (which was rapidly becoming an excellent string-theory physical model 
), I decided to use Microsoft’s VS Code to allow me to develop on my Windows box and sync things between the main system, the robot, and the base GitHub repo.
Because of my abysmal lack of knowledge about distributed development environments1, it rapidly turned into a “Hawking’s Singularity”2 () that swiftly degenerated into chaos. I tried a number of stupidly complex ideas until I eventually figured out how simple the solution actually was.
I ultimately figured out how to make it work, (which I documented elsewhere here), and which I summarized on Stack Overflow.
Viz.:
It is very likely that you already know all about this, and if you do - I apologize for insulting your intelligence.
Otherwise, I hope this helps you organize your research workspace better.
Footnotes:
As you may have already guessed, I am not a “professional” developer by any stretch of the imagination, primarily being a “black-box” SQA person.
As a consequence, my actual knowledge and experience in managing a development environment of any reasonable size was somewhere between zero, zilch, and nada.
The result was a mish-mash of untried theories and poorly written explanations that I had read on-line untill I figured it out and clarified it on Stack Overflow. It appears that there was a real need for that clarification as that one posting alone seems to have become extremely popular and has boosted my “reputation” immeasurably.
Actually, I believe it’s called a “Schrodinger’s Singularity”, but I think Stephen Hawking doesn’t, (and didn’t), get the love he deserved and was blatantly skipped-over for a Nobel Prize because the Nobel Prize committee didn’t want someone with his disabilities “sullying” the Nobel Prize ceremony. (
)
@jimrh You are correct! I have set up VS Code on my Widows laptop to tunnel into the VS Code CLI on the raspi. All the code get’s written on the laptop but it “appears” on the raspi. Pretty clever tech really!