I think the answer to this question should be: No. However I hope to be corrected.

I'd like to edit our database using a mixture of YAML markup + Doctrine createTables() and Navicat editing. Can I maintain the inheritance which is marked up?

Example (4 steps, at step 4, Doctrine is in no way able to re-create the inheritance schema... or is it?):

Step 1: Create YAML with inheritance

---
Entity:
  columns:
    username: string(20)
    password: string(16)
    created_at: timestamp
    updated_at: timestamp

User:
  inheritance:
    extends: Entity
    type: column_aggregation
    keyField: type
    keyValue: 1

Group:
  inheritance:
    extends: Entity
    type: column_aggregation
    keyField: type
    keyValue: 2

Step 2: Create tables using Doctrine (and drop/create db if nessecary)

Created sql:

CREATE TABLE entity (id BIGINT AUTO_INCREMENT, 
username VARCHAR(20), 
password VARCHAR(16), 
created_at DATETIME, 
updated_at DATETIME, 
type VARCHAR(255), 
PRIMARY KEY(id)) ENGINE = INNODB

Step 3: Edit table using Navicat Step 4: Refresh YAML file because of 'external' edits...