I've come across the problem that I've made some templates that are meant to be used independently from eigen (i.e. cannot depend on eigen) that are none-the-less in need of eigen alignment when used with eigen types to conform to stated eigen alignment rules.

Is there any known solution to this? In some cases I can change some of the data members to references to avoid the problem, but others probably not.

you can use types that does not require alignment, like:

Eigen::Matrix<double,4,1,Eigen::DontAlign> instead of Eigen::Vector4d... The downside is that you lost vectorization for these precise objects.

Do they play well with types are aligned? For instance, can I do the following safely?:

Eigen::Matrix<double,4,1,Eigen::DontAlign> foo;
Eigen::Matrix<double,4,1> bar;

foo.dot( bar );

sure, they are fully compatible.