MySQL 5.6 Online DDL lead to to much table-metadata-locks when I just add index
There are good reasons ALGORITHM=INPLACE may not be used and switches to ALGORITHM=COPY.
REASON #1
In the link you gave in the question, there is a chart that shows the following:

Adding a FULLTEXT index trigger a table copy is not supported for online operation
Many operations can revert to copy because it says in the notes Although ALGORITHM=INPLACE is allowed, the data is reorganized substantially, so it is still an expensive operation.

Some online DDL may still lock and copy because of an index's interaction. Don't forget that each BTREE entry in a secondary index has a hook back to the primary key. Adding a new secondary index may induce row level locks and index locks.
REASON #2
According the limitations page : InnoDB tables created before MySQL 5.6 do not support ALTER TABLE ... ALGORITHM=INPLACE for tables that include temporal columns (DATE, DATETIME or TIMESTAMP) and have not been rebuilt using ALTER TABLE ... ALGORITHM=COPY.
I am sure there are other reasons that can be researched an discussed along these lines.