Hello @Maciek
It looks like a bug on our side, we are going to fix it as soon as possible. As an workaround, try to add one more dummy linker file in the {toolbox_path}\mbdtbx_s32k11x\src\linker\gcc, like in the picture below:


It appears that the last file is ignored and the linker file list from dropdown inside the configuration block is not updated correctly.
But as a mention, when using Rappid Bootloader to flash the application on the target, you do not have to change manually the linker file. If you check that Default target memory definitions, then automatically the S32K118_25_flash_bam.ld linker file is going to be used, without any other modifications. In case you have your own custom linker file, then you must uncheck Default target memory definitions option and put your own custom linker file in the {toolbox_path}\mbdtbx_s32k11x\src\linker\gcc path. Also, your custom linker file name must have the following pattern: platformName_sramSize_memory_*.ld where platformName is the name of the MCU (in your case S32K118), sramSize is the memory size of your MCU(for S32K118 is 25) and memory represents the memory where the application is deployed, flash or ram. As an example: s32k118_25_ram_myOwnCustomLinker.ld
Yes, the steps that you`ve enumerated when using Rappid Bootloader are correct, with the upper mention. And indeed, UART1 and CAN0 are the communication instances used by the bootloader to listen on.
As for the last question, the pins for UART1 that are used for the bootloader, you could use PTC6 - J4[2] or PTC8 - J4[6] as RX and PTC7 - J4[4] or PTC9 - J4[9] as TX, but you have to use also an external USB2Serial converter because those pins are not routed to the microUSB port from the S32K118-EVK.

You can flash the S32K116_S32DS_UART0_CAN0.rbf file on the S32K118-EVK and you will be able to use the UART0 TX and RX pins that are routed to the microUSB from the EVK. That will work because both S32K116 and S32K118 have the same UART0 RX and TX pins.
Hope this helps!
Regards!
Stefan.