Hi,
Thanks for your feedback.
We are showing Config Tools inside S32 Design Studio, that is the tools we mainly use for this platform.
On regards of the custom timer, it is related to OSIF_COUNTER_CUSTOM option, you could try and verify if this provides the functionality you are looking.

As said before, since we do not see any compatibility from our side with RTX, we cannot confirm the functionality. Below will be a thread that seems to talk about a similar topic, could be of use:
Using S32SDK: osif conflicts with my custom schedu... - NXP Community
Please, let us know.