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Could you describe the situation where timeout settings are ignored in matrix projects? I assume you mean a job which Jenkins calls a "multi-configuration project".
I defined a multi-configuration project, set the timeout to 1 minute, and attempted to clone a 6 GB repository to Windows 6.1, Windows 6.2, Debian 7.5, and Debian Testing. The flyweight repository (created on initial job start) correctly honored the timeout and stopped the clone operation after 1 minute.
I then modified the job definition to use a reference repository and to create the initial flyweight repository on the master server so that it could use that reference repository for a faster clone. The flyweight repository was cloned successfully and the jobs started on the other machines. The two Windows machines failed their clone in 1 minute because they don't have a copy of the reference repository. As far as I can tell, the timeout option is honored by multi-configuration projects the same as it is honored for other projects.