breakdown voltage in BJT
For the common-base configuration, the base is common ("grounded") and the collector-base breakdown voltage is determined with the emitter open so, as you write, the breakdown voltage is essentially that of a PN junction.

For the common-emitter configuration, the emitter is common and the collector-emitter breakdown voltage is determined with the base open.  In this mode, the base width modulation and impact ionization effects enhance the avalanche breakdown of the collector-base junction leading to a lower breakdown voltage.

See, for example, this.