Clarification concerning the blog post
The feature you are basically looking at is
fast index creation. This features speeds up the creation of secondary indexes to InnoDB tables, but it is only used in very specific cases. For example the feature is not used while
OPTIMIZE TABLE, which can therefore be dramatically speed up by dropping the indexes first, then run
OPTIMIZE TABLE and then recreate the indexes with
fast index creation (about this was the post you linked).
Some kind of automation for the cases, which can be improved by using this feature manually like above, was added to Percona Server as a system variable named
expand_fast_index_creation. If activated, the server should use fast index creation not only in the very specific cases, but in all cases it might help, such as
OPTIMIZE TABLE — the problem mentioned in the linked blog article.
Concerning your question
Your question was actually if it is possible to save InnoDB tables in a custom order to speed up specific kind of queries by exploiting locality on the disk.
This is not possible. InnoDB rows are saved in pages, based on the clustered index (which is essentially the primary key). The rows/pages might be in chaotic ordering, for which one can
OPTIMIZE TABLE the InnoDB table. With this command the table is actually recreated in primary key order. This allows to gather primary key local rows on the same or neighboring pages.
That is all you can force InnoDB to do. You can read the manual about clustered index, another page in the manual as a definite answer that this is not possible ("ORDER BY does not make sense for InnoDB tables because InnoDB always orders table rows according to the clustered index.") and the same question on dba.stackexchange which answers might interest you.