Hello @oeren5 ,
Let's take them point by point.
For the first main question regarding what is on and what is off when the uC runs in the low power modes, I strongly suggest having a look at the S32K1XXRM Table 39-1. Chip power modes and table Table 39-4. Module operation in available power modes
From those two tables, you will get that the LPTMR timer is fully functional VLPR but only if the SIRC clock is used, while in VLPS it runs in Async operation. This means that the peripheral is fully functional if the clock source remains enabled.

Now, SIRCDIV2 can be the source clock for the LPTMR so having a look again at that table, we get that the SIRC is Fully Functional, no matter what power mode is active.
No, that we have this information, I have integrated the LPTMR timer functionality in the model that @rathi_tg was kind enough to share previously.
Now, what is important is to configure the LPTMR in the ticks to know exactly what Prescaler is used in order to be able to transform back from ticks to seconds. So I will select the maximum compare value, FFFF and select ticks.

Now, in the next tab, in Advanced, I select the SIRCDIV2 as main clock source and the prescale value to be 1024. What this means is that by dividing the SIRCDIV2 by 1024 I got 7815. (SIRCDIV2 is the name of a clock signal which, in our case, is equal to the 8MHZ the SIRC frequency. SIRCDIV2 it doesn't mean that the clock is 4MHz). So after one second, the timer will store 7815. This means that we can count up to 8.35 seconds until the LPTMR counter overflow occurs. If you increase the prescaler you will be able to measure a large amount of time.

With these settings, I am going to use the VLPS mode. In the Callback_before I am going to start the counter, while in the Callback_after I am going to get the counter value and to transform it back to seconds.

In the callback after, I firstly turn off the RED LED, and them Get the Cunter Value. To transform the value back in seconds, I have to apply the formula: time = Counter / (SIRCDIV2/prescaler).

I can check that the math is good, by using a Logic Analyser. I will attach the logic analyzer to the RED led which is turned on while the board runs in VLPS. You can see that the values are roughly the same.
I have attached both model and FreeMaster project. If you have further questions, feel free to post here.
Hope this helps,
Marius