Hello, @RushikeshK_DC.
Initially I will approach the DIO_Test00 model for which you tried to generate code based on the DIO component. From what I can see from the model, the hardware part used to generate code is S32K344-Q257. Is this aspect correct?
Assuming that the hardware part is correct, from what I can see in the configuration project there is a discrepancy between the configuration of the pins in the Port, Pins and Dio components. A good reference to understand the connection between the Port and Dio components can be found at the following link, even if it is for the EB Tresos configuration tool, the concepts are similar.
Referring to your configuration, I can see that the only change in the Port component is related to LED1 which has MSCR 29, which also corresponds to RGBLED0_RED.

In the Dio section, I found LED1, LED2 and LED3 configured as PTG_L.

On the other hand, in the Pins section, I notice that the same pins are incorrectly configured, being assigned to the Adc_Pins_MBDT functional group. Instead, they should be set in the functional group corresponding to Dio, namely Dio_Pins_MBDT.

Moreover, MSCR registers must be synchronized between Port and Pins components, to ensure the connection between software and hardware configuration.
As a last mention related to your application, for the S32K344-Q257 board all the available LEDs are already configured in the default configuration project, namely RGBLED0 and RGBLED1.
Now, on the other hand, related to the s32k344_pwm_led_s32ct model, I notice similarities in the configuration of the pins with the DIO_Test00 model. The PWM signals you want to configure use eMIOS instance 1 and channels 19, 20 and 21, but they are functionally assigned to the wrong group, they must be set in Pwm_Pins_MBDT.

In the Pwm component the PWM channels are correctly set, according to the eMIOS instances used.

But in the Port component, the pins you are trying to use are not configured correctly.

I hope this helps.
Regards,
Dragos