Using SqlYog Enterprisse 8.17, I ran a Schema Compare on a source and target where one of the tables had auto-increment set on the primary key (id) column and the other did not. The comparison failed to report any differences on this table. I repeated this issue several times to confirm.
Source table:
CREATE TABLE `atest1` (
`id` int(10) NOT NULL,
PRIMARY KEY (`id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
Target table:
CREATE TABLE `atest1` (
`id` int(10) NOT NULL auto_increment,
PRIMARY KEY (`id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;