Would you lay out your logic (pun intended) a bit more? In what cases does doing from 8-bit bytes to 9-bit bytes result in something like a 2X penalty?

One possibility would be bit-indexed addressing. For the 9-bit case, yes, such an index would need 4 bits. If one wanted to keep nice instruction set encoding nice and clean, that would result in an underutilized 4th bit. Coming up with a more complex encoding would cost silicon.

What other cases are you thinking of?

> In what cases does doing from 8-bit bytes to 9-bit bytes result in something like a 2X penalty?

Self-correction: In what cases does going from 8-bit bytes to 9-bit bytes result in a penalty, and how much is it?