These issues arise only with \ref FixedSizeVectorizable "fixed-size vectorizable Eigen types" and \ref StructHavingEigenMembers "structures having such Eigen objects as member". For other Eigen types, such as Vector3f or MatrixXd, no special care is needed when using STL containers.
STL containers take an optional template parameter, the allocator type. When using STL containers on \ref FixedSizeVectorizable "fixed-size vectorizable Eigen types", you need tell the container to use an allocator that will always allocate memory at 16-byte-aligned locations. Fortunately, Eigen does provide such an allocator: Eigen::aligned_allocator.
Note that here, the 3rd parameter "std::less<int>" is just the default value, we only had to specify it because we needed to specify the allocator type, that is the 4th parameter.
The situation with std::vector was even worse (explanation below) so we had to specialize it for the Eigen::aligned_allocator type. In practice you \b must use the Eigen::aligned_allocator (not another aligned allocator), \b and \#include <Eigen/StdVector>.
<span class="note">\b Explanation: The resize() method of std::vector takes a value_type argument (defaulting to value_type()). So with std::vector<Eigen::Vector4f>, some Eigen::Vector4f objects will be passed by value, which discards any alignment modifiers, so a Eigen::Vector4f can be created at an unaligned location. In order to avoid that, the only solution we saw was to specialize std::vector to make it work on a slight modification of, here, Eigen::Vector4f, that is able to deal properly with this situation.