Why purpose-built cargo submarines remain poor transports

Can an effective cargo submarine be made viable if it is designed for transport from the start?

Not very well; the German First World War examples show that purpose-built cargo submarines still make poor transports.

Designing a submarine for cargo from the outset does not remove the volume, cost, and handling penalties imposed by underwater operation. The Kaiserliche Marine's First World War transport submarines are real examples that never became especially effective cargo vessels.