Confusion with MC34063 Vsat
When digging through the datasheet I stumbled upon the same problem. The datasheet gives the answer to your question.

Look on page 9, down on the schematic. You can see that pins 1 and 8 are directly connected, consequently, if you look on page 5, table in point 7.6 you can see that test conditions for Darlington pair is when mentioned pins are directly connected. When you look closer at the internal schematic of the IC itself you will realize, that this connection makes Q1 and Q2 of the IC a Darlington pair. What I would do in such situation is take Vce(sat) of the Darlington connection to my calculations for inverting config, as long as you won't use external switch and hook up pins 1 and 8 together.

Have a nice design,
Maciek

EDIT: Saturation voltage of the Darlington pair is only applicable for the step-down and inverting topologies, for other use the other one given in the datasheet. For more info watch https://www.youtube.com/watch?v=qGp82xhybs4