Michael, read-modify-write issue doesn't apply to S08 port interrupt. RMW problem applies only to registers, which include several interrupt flags, not the single. No matter, is flag clearable writing '0' or '1' to flag, RMW is bad when single register contains more than one such flags. Example:
Both flag bits are set. Now you write one just to bit 1, and "preserve" one in bit 2. As a result you clear both flags instead of one, because you made CPU writing ones to both flags. It doesn't matter, is it BSET instruction or sequence of LDA OR STA, in both cases you get wrong results. You need to code it so that one is written only to flag you want to clear.
Since PTASC has single flag bit, it is fine to use RMW.
Bert, you didn't say what exactly isn't working, but PORT interrupt has single latch for all unmasked PTAPSx bits! See 6.3 Pin interrupts. It means that you need to provide that you service A6 edge (get to interrupt and clear interrupt flag) before A7 edge, and vice versa, else you will loose interrupt events. Isn't it your issue?