Does not sound odd, but in your case you will store results on disk, rather than in memory? That means that there might be some overhead in (de-)serialization and also some restrictions on what kind of data can be stored as an intermediate result?
I don't think serialization is a problem either. It is possible to make data structures that always exist as a single span of memory, so that they don't have a separate serialized representation. Most data structures are better served like this anyway, since prefetching and linear memory access is a huge speedup over pointer chasing. Building a data structure out of many separate heap allocations will also slow it down.