Was playing with moodle.org (upgraded from 1.9 recently as you know), and detected this differences from clean install:

• missing index: CREATE INDEX blocinst_par_ix ON block_instances (parentcontextid);
• differences in columns:
  • blockinstances->defaultweight size = 3 @ moodle.org (should be 10)
  • block_positions->blockinstanceid missing unsigned property

Surely minor details to be fixed on upgrade to make no differences between upgraded/installed sites. Note the index can have impact in performance and the size could (in theory) lead to storage problems too.

Triaging to STABLE, would be great to have this fixed in next iteration. Ciao