Recently had this issue. When I enabled my custom theme some files were missing and Drupal threw some errors and warnings. After adding the files everything worked fine except the Main page content block was missing.
To fix, I did the following:
- Set Bartik as the default theme
- Navigated to the block interface and configured the Main page content block (which was showing now that Bartik was the default theme)
- My custom theme was still enabled so it showed up in Region settings and I was able to select a region
Set my custom theme as the default again and all was good. Main page block was showing again.