Here's the output from the console where the linker gets invoked:
Building target: RTCP_Host_BL.axf
Invoking: MCU Linker
arm-none-eabi-gcc -nostdlib -L"C:\Sources\NXPBootloaderPoC\RTCP_Host_BL\libs" -Xlinker -Map="RTCP_Host_BL.map" -Xlinker --gc-sections -Xlinker -print-memory-usage -Xlinker --sort-section=alignment -mcpu=cortex-m4 -mfpu=fpv4-sp-d16 -mfloat-abi=hard -mthumb -T "RTCP_Host_BL.ld" -L ..\ -o "RTCP_Host_BL.axf" ./startup/startup_mkv31f51212.o ./source/Test_Proj.o ./board/board.o ./board/clock_config.o ./board/peripherals.o ./board/pin_mux.o ./CMSIS/system_MKV31F51212.o -larm_cortexM4lf_math
arm-none-eabi-gcc.exe: error: RTCP_Host_BL.axf: No such file or directory
make: *** [RTCP_Host_BL.axf] Error 1
11:26:49 Build Finished (took 3s.866ms)
The reason why I turned off the managed linker script mechanism is to keep the start addresses and lengths of the bootloader and application images in the same space. If I used the Memory Configuration Editor in the project settings, it would be REALLY easy for a developer later on to change an address or length in one project (application or bootloader) and forget to change the addresses in other project.
I have a common linker file that is included by the main linker scripts for the bootloader and application, like this horrific diagram shows:

Addresses.ld contains the following:
__TOTAL_FLASH = 0x00040000;
__BOOTLOADER_START = 0x00000000;
__BOOTLOADER_LENGTH_BYTES = 0x00005000;
__APPLICATION_START = __BOOTLOADER_START + __BOOTLOADER_LENGTH_BYTES;
__APPLICATION_LENGTH_BYTES = __TOTAL_FLASH - __BOOTLOADER_LENGTH_BYTES;
MEMORY
{
/* Define each memory region */
BOOTLOADER_FLASH (rx) : ORIGIN = __BOOTLOADER_START, LENGTH = __BOOTLOADER_LENGTH_BYTES
APPLICATION_FLASH(rx) : ORIGIN = __APPLICATION_START, LENGTH = __APPLICATION_LENGTH_BYTES
SRAM_UPPER (rwx) : ORIGIN = 0x20000000, LENGTH = 0x8000 /* 32K bytes (alias RAM) */
SRAM_LOWER (rwx) : ORIGIN = 0x1fffc000, LENGTH = 0x4000 /* 16K bytes (alias RAM2) */
}The linker script for the bootloader uses the BOOTLOADER_FLASH memory definition. The linker script for the application uses the APPLICATION_FLASH memory definition.
This way, a future developer has less of chance of screwing up the memory locations, since the values for the start addresses and lengths are all contained within a common, shared file. It also eliminates duplication, and duplication drives me up the wall.