Hi,
It is good to know that is working now. You are right, the reason why this Pins are configured in open-drain when they are like an output is because they are used for the SDA and SCL of the I2C where is necessary to have the signals as output/input.
Indeed the normal LDD component for the Bit does not support the Pull enable functionality on the pin. The workaround that I can tell is to use an extra component: the Init_PORT component; this kind of components only generate an init() method for the modules but have all the configuration registers.
Check the image below to see how should be the Init_PORT component configured to allow the Pull functionality on a Pin. You can also write the line PORT_PUEL |= PORT_PUEL_PTAPE3_MASK; in your code in some part where PEx expert will not let you to write your code, if is in somewhere else PEx will erase that line every time you use the Generate Code button. I think is a better practice to add the Init_PORT component, since it is just one component to enable the pull-up to all the Ports.

:smileyalert:Also, you need to have in mind the note for the PTAPE3 that you can find in the reference manual:
NOTE: When configuring to use this pin as output high for IIC, the internal pullup device remains activewhen PTAPE3 is set. It is automatically disabled to save power when output low.
Hope this information can help you.
Regards,
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