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For the record, 2.5.8 was extensively tested on multiple Linux variants as well as multiple stacks on Windows. Somehow, you are skipping the autoloader if Xmf\IPAddress can't be found. The autoloader is started when class/xoopsload.php is included.
For the database transactions, we stay in the default autocommit mode unless the application (module) says otherwise. Since the core uses MyISAM by default, there is no benefit to an explicit transaction, so we don't interfere. For application use, forcing a transaction would break things, since in MySQL transactions cannot nest. It also gets complicated if you are using DDL in the application.
The autocommit behavior already accomplishes what you suggest adding, and the application can easily change that by issuing its own START TRANSACTION.
Lots of the details change in 2.6, and explicit transactions are already used there.