Mysql – thesql workbench migration changed the database. Can I trust it

I'm migrating a large production database(s) from mysql 5.5 to 5.6.
Used Mysql Workbench Migration Wizard which creates a shell script to run on source and taget machines.

The process worked well but there are major changes to the database:

For example:

1. Changed order of fields in primary key
   PRIMARY KEY (ru_sid,ru_rule_id), => PRIMARY KEY (ru_rule_id,ru_sid)

2. Messed encoding while the data is expected to be utf8
   I did a query of the same data in the original and new server and the output is different:
   Pré-Home Flash Sales => Pré-Home Flash Sales

Possibly there are other changes.

My question is – how can I tell if the migration is trustable. I cant check every table to see if changes in the index will not break something in my code.
Can the workbench migration be trusted ?
Is there a better way to do the migration? What would you do?

EDIT:
Create statement before:
(I removed the fields that are the same in the before and after)

CREATE TABLErules(
ru_rule_idint(10) unsigned NOT NULL AUTO_INCREMENT,
ru_titlevarchar(254) COLLATE utf8_unicode_ci NOT NULL DEFAULT '',
ru_datatext COLLATE utf8_unicode_ci NOT NULL,
ru_namevarchar(64) COLLATE utf8_unicode_ci NOT NULL,
ru_tagsvarchar(64) COLLATE utf8_unicode_ci DEFAULT '',
ru_priorityvarchar(12) COLLATE utf8_unicode_ci NOT NULL DEFAULT '1',
PRIMARY KEY (ru_sid,ru_rule_id),
KEYnum(ru_rule_id) USING BTREE
) ENGINE=MyISAM AUTO_INCREMENT=9998 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;


Create statement after:

CREATE TABLErules(
ru_rule_idint(10) unsigned NOT NULL AUTO_INCREMENT,
ru_titlevarchar(254) CHARACTER SET utf8 NOT NULL DEFAULT '',
ru_datatext CHARACTER SET utf8 NOT NULL,
ru_namevarchar(64) CHARACTER SET utf8 NOT NULL,
ru_tagsvarchar(64) CHARACTER SET utf8 DEFAULT '',
ru_priorityvarchar(12) CHARACTER SET utf8 NOT NULL DEFAULT '1',
PRIMARY KEY (ru_rule_id,ru_sid),
KEYnum(ru_rule_id)
) ENGINE=MyISAM AUTO_INCREMENT=9954 DEFAULT CHARSET=utf8 COLLATE=utf8_unicode_ci;