You can refer to the thread: How to configure CX3 MIPI receiver configuration for streaming RAW10 4096x3072 @ 10 fps ?
It explains all the different aspects and calculations that should be taken care of using CX3 MIPI Configuration Utility.
First of all, the version of the Cx3 Configuration Utility that is being used has some bugs and the utility can sometimes gives errors like this.
But, you can ignore these errors as your calculations are correct.
You can use CSI Clock= 250MHz - 500MHz with the same configuration as above but you will need to use the FIFO Delay value = 241-511.
But don't exceed the CSI Clock above 500MHz as it is not recommended.
I have checked these settings and they work fine with CSI Clock = 250MHz and FIFO Delay= 241.
So, you can neglect the errors and go ahead with your application and the application willl work just fine.