Persistent Homology (PH) offers stable, multi-scale descriptors of intrinsic shape structure by capturing connected components, loops, and voids that persist across scales, providing invariants that complement purely geometric representations of 3D data. Yet, despite strong theoretical guarantees and increasing empirical adoption, its integration into deep learning for point clouds remains largely ad hoc and architecturally peripheral. In this work, we introduce a unified design space for Persistent-Homology driven learning in 3D point clouds (3DPHDL), formalizing the interplay between complex construction, filtration strategy, persistence representation, neural backbone, and prediction task. Beyond the canonical pipeline of diagram computation and vectorization, we identify six principled injection points through which topology can act as a structural inductive bias reshaping sampling, neighborhood graphs, optimization dynamics, self-supervision, output calibration, and even internal network regularization. We instantiate this framework through a controlled empirical study on ModelNet40 classification and ShapeNetPart segmentation, systematically augmenting representative backbones (PointNet, DGCNN, and Point Transformer) with persistence diagrams, images, and landscapes, and analyzing their impact on accuracy, robustness to noise and sampling variation, and computational scalability. Our results demonstrate consistent improvements in topology-sensitive discrimination and part consistency, while revealing meaningful trade-offs between representational expressiveness and combinatorial complexity. By viewing persistent homology not merely as an auxiliary feature but as a structured component within the learning pipeline, this work provides a systematic framework for incorporating topological reasoning into 3D point cloud learning.