1) The pipe to the left looks like a vent. The pipe to the left of the flange could be the WC vent or wet vent (Depending of the diametre of that pipe). The pipe on the right might be a wet vent for the shower/bathtub rough-in. Its hard to tell without knowing your basement layout.
In my area, we have to connect all the vents at the rough-in stage with the appropriate T's, whether you finish the basement or not
2) If you don't want to dig into the cement and extend those 2 pipes straight into the wall, you could cut the pipes at about 3/4" off the floor and offset them with 2 - 45's into the wall
3) The drain box seems to be roughed in for a bathtub. If you want a shower, you may end up chopping some cement to relocate your new shower drain.
I hope I help from what I could see