Jer,

Sorry for my laziness to analyze the transcription...
Here's the one you can hear how iReal player play your changes from the transcription.

Midnight Mood fragment (de la Fuente-Jer) - Joe Zawinul

This IS real chord chart but I feel iReal player's limitations that you mentioned partially make it sound a bit awkward to me.

Here, after reading your message,
I modified my chart becoming closer to the transcription and the performance.

Midnight Mood (Evans) - Joe Zawinul

I moved the pedal 5th Ab to the latter (2nd or 3rd) beat...sorry, but it still remains.
I can't help but keep the 5th pedal (even the root Db is the lowest bass note) in the chart,
because the over all Bill's performance emphasizes the low 5th notes
in the first seven bars in the melody in each section:
5th Ab together with root Db in section A (key Db),
and 5th A and C in B and C sections (key D and F) respectively.

Cheers,
shin1ro