Neither. That's pretty much the case suggests The situation is similar to what you thought it was. That is indeed the case suggests You're right. That is exactly how the situation is.
The basic sentence is That is the case, and the additional words are modifying it in some way, so it works best if just one modifier is used. A second is at best redundant and at worst contradictory. That is indeed the case. That is very much the case. That is pretty much the case. That is generally the case.