Shouldn’t be a problem. You can import PPro sequences directly into Adobe Media Encoder by choosing File > Import Premiere Pro Sequence. When you highligt a .pproj file, you can choose which sequences contained therein you want to export. You can queue these up, change the export settings and start the process.
If you want to make sure you’re exporting the correct range (work area, for example), you open the projects in PPro, go to export and then choose “Add to queue” or something similar instead of pressing the “Export” button. This will send the timeline with the correct export range to Media Encoder export queue.