Basement Bathroom Rough-In Configuration
I think you don't "have to" break up the concrete.


Let's say your shower/tub extends out 30inches.  Whether you have to break up concrete around shower pan or for tub depends on what you install.  The last few pans I installed in basements met above grade -slightly.  Also note that you will have to find a pan/tub that fits those exact dimensions or you will have to move it or make your own pan.  Breaking concrete and moving the PVC over a few inches is a very DIY job.
Based on the 30 inches above you would have 15.5" to shower from toilet and per your picture 14.5" on the other side.  You would have to check with your local inspector but this would pass where I live.  It will be kind of tight but not terrible.  Toilets are about 15 inches wide so you are going out 7.5 inches on each side.  So you have about 6-7" on each side - most towns require 6" by me.  When you add in your drywall you are getting very close but still within most regulations.
You put up privacy wall that extend past vertical pipe.  I would frame this wall with 2x6 so plumbing access is easier.  Pop a vanity on opposite side of toilet and you are all set.  


This had to be the configuration that was previously given to your town if the work was permitted.  I suggest you ask them for any paperwork associated with it.  I know I have to give detailed sketches before any rough-ins so as long as they did things the right way there is probably a sketch of your bathroom.  

My opinion... Toilet space is kind of tight but not horrible.  I have seen toilets 1 inch from walls.  You still crap in them.  This isn't as bad.  I like the layout though.  One person can take a crap without being in the other person's face.  Note that having this privacy wall will trap moisture so you better have a good vent fan by the shower/toilet.  I like it.  If you are tight on space I would try to work with this.  If you can add space then I might think about moving the vertical stack over a few inches - really an hour or two of work at most.