We introduce a novel learning-based method for encoding and manipulating 3D surface meshes. Our method is specifically designed to create an interpretable embedding space for deformable shape collections. Unlike previous 3D mesh autoencoders that require meshes to be in a 1-to-1 correspondence, our approach is trained on diverse meshes in an unsupervised manner. Central to our method is a spectral pooling technique that establishes a universal latent space, breaking free from traditional constraints of mesh connectivity and shape categories. The entire process consists of two stages. In the first stage, we employ the functional map paradigm to extract point-to-point (p2p) maps between a collection of shapes in an unsupervised manner. These p2p maps are then utilized to construct a common latent space, which ensures straightforward interpretation and independence from mesh connectivity and shape category. Through extensive experiments, we demonstrate that our method achieves excellent reconstructions and produces more realistic and smoother interpolations than baseline approaches.