This is just a little hard to understand. The ZRTSI II is sending the same UP/DOWN/STOP RTS commands as the remote. The response direction for the motor is set in the RTS receiver. All that's programmed in the ZRTSI II is the channel number on which to send the command.
I believe you when you say it's operating the way you say it is. It's just hard to understand how the same UP/DOWN command sent by the remote is being treated as DOWN/UP when sent by the ZRTSI II interface. I've never seen this behavior in any of our SOMFY Glydea drapes, Somfy remotes, Somfy myLink, or Somfy ZRTSI II.
What you seem to be saying is that the remote is sending the DOWN command when the UP button is pressed, and the UP command when the DOWN button is pressed. I've never taken one of the remotes apart, not sure if it's possible to install the circuit board upside down so that the wrong button is associated with the UP switch.
There are two community ZRTSI II drivers - this one and the one by Justin Walker (@augoisms). I happen to be using the one by Justin Walker. I can't imagine why the two drivers would behave differently on this point, but you might try switching drivers. Justin Walker's driver is here:
https://raw.githubusercontent.com/augoisms/hubitat/master/somfy-zrtsi/somfy-zrtsi.driver.groovy
See:
