No, you do not. You should organize your BioProjects the most appropriate way for your research effort.

From 12 November 2014, multiple Project data types can be selected for a project in the submission system.

To merge genome sequencing and transcriptome analysis projects, select both 'Genome Sequencing' and 'Transcriptome or Gene Expression' for the Project data type. One material is allowed for the Material, so select 'Other'.

Another way is to register 'Genome Sequencing' and 'Transcriptome or Gene Expression' as separate projects and unite them by an Umbrella BioProject.