It is possible to split up the policy-file, just by creating the subfolders with the content XML files. Achieving part two, pulling the subfolders from AEM, is not possible. I don't have a solution for this problem, but I thought it might be interesting to understand the root cause:
Pulling from AEM using the repo tool, relies on vault in the background. When
vault serialises the nodes, it decides to aggregate them fully, partly or not at all based on the node type and nt:unstructured aggregates the entire subtree into one file. When saving a policy in AEM
all nodes within the configuration are updated/overwritten to nt:unstructured. That happens even if the node type was changed before! When pulling the policy, all nodes are aggregated into one large file rather pulling them into multiple, individual files. There is no way to configure that otherwise.