Hello @RNJ
First of all, let’s set the stage. As you already know, the MBDT blocks for accessing and controlling hardware peripherals are built on top of the NXP RTD MCAL AUTOSAR layer. This means that all functions exposed through the Simulink peripheral blocks (ADC, PWM, etc.) must comply with the AUTOSAR MCAL specification.
The RTD package contains two layers:
- The Low-Layer Driver:
- Similar to a classical SDK;
- Provides full access to hardware features;
- Allows configurations that AUTOSAR does not define
- Suitable for non‑AUTOSAR applications
- The High-Layer Driver (or the MCAL layer):
- which shall be compliant with AUTOSAR standard;
- Only exposes features that AUTOSAR explicitly supports;
- Any hardware feature not defined in AUTOSAR is suppressed or restricted.
If some configurations are available on the Low-Layer Driver and are not compliant with the AUTOSAR standard, the MCAL Layer will not expose them. In the same way, the S32 Configurations Tool will block the settings which are not compliant with AUTOSAR. In other words, If some peripheral setting or configuration is available on the hardware, the AUTOSAR MCAL Layer could "cancel" it, if it is not compliant.
Going back to your initial inquiry, I can say that I am not an AUTOSAR expert, but I have done some research and I have found out the following AUTOSAR PWM Driver requirement.

I honestly don't know why, but it seems that AUTOSAR PWM driver does not support the half-cycle reload.
When you select PwmDutyCycleUpdatedEndperiod or PwmPeriodUpdatedEndperiod, AUTOSAR requires that updates occur only at the end of the PWM period. This maps directly to full‑cycle reload only in eFlexPWM. Because half‑cycle reload contradicts AUTOSAR semantics, the S32CT blocks it.
I also had a look within the RTD to see exactly how it translates in C code. The S32CT generates the configuration structures and files inside the generate folder within the {modelName}_Config directory. On the FlexPWM configuration structure, the reload is set according to what the user is setting within the Pwm/PwmChannelConfigSet/FlexPwm Modules in S32CT, as in the image below.

However, the PwmDutyCycleUpdatedEndperiod and PwmPeriodUpdatedEndperiod are AUTOSAR-level macros used directly in the Pwm RTD driver. For example, the Pwm_SetDutyCycle function calls within it the Pwm_Ipw_FlexPwm_SetDutyCycle. Then, it checks PWM_DUTYCYCLE_UPDATED_ENDPERIOD and will set the LDOK bit accordingly. Refer the the following image.

The above highlighted function will load the effective duty cycle values in the module registers, based on the last function argument. FALSE means next PWM reload and TRUE means update immediately.
As a conclusion, the S32CT enforces AUTOSAR PWM driver rules. When you select “PwmDutyCycleUpdatedEndperiod” or “PwmPeriodUpdatedEndperiod”, the AUTOSAR specification requires that updates occur only at the end of the PWM period.
What you could do to overcome this driver limitation is to directly overwrite the SMn_CTRL[LDMOD] register in your model, using custom code blocks. But, I am not sure if it will work. It has to be tested. However, to overcome the PwmDutyCycleUpdatedEndperiod macro check from the Pwm_SetDutyCyle function, the duty cycle values has to be as well directly written to the SMnVALx registers, using custom code blocks.
Hope this helps!
Best regards!
Stefan.