Revision 2 has an error in the silkscreen for J200, correct signal allocation is as documented in Table 2.
DGI GPIO header can not be disconnected from target, this revision does not have R215, R216, R217, and R218.
The figure below shows the evaluation kit overview for revision 2 of the kit.
Figure 1. ATmega324PB
Xplained Pro Evaluation Kit
Overview Revision 2