In any case this does not prevent combining the two drafts, which will be much easier for readers, e.g.:
Part 1: threats that only affect network layer solutions Part 2: threats that affect both network and transport layer solutions Part 3: threats that only affect transport layer solutions
Yes, or other option is to make an analysis for IP layer solutions and another for transport layer, but in any case IMHO we should clearly undestand the differences between the two cases.