I've faced the same issue today and observed the same problem that you described:
"Looking at the image the initialisation data should be loaded after the image to the addresses specified by the table in Region$$Table$$Base."
It seems that although very similar, the ELF file generated by armlink is a bit different than the ELF generated by GCC.
Anyway, I've found a workaround for that.
Checking my main.elf, I noticed that armlinker stored the initialization data into the ER_RW section:
arm-none-eabi-readelf.exe" -S main.elf
There are 16 section headers, starting at offset 0x122b0:
Section Headers:
[Nr] Name Type Addr Off Size ES Flg Lk Inf Al
[ 0] NULL 00000000 000000 000000 00 0 0 0
[ 1] ER_RO PROGBITS 20000000 000034 001358 00 AX 0 0 4
[ 2] ER_RW PROGBITS 20002000 00138c 0000cc 00 WA 0 0 4
[ 3] ER_ZI NOBITS 200020cc 001458 0004e8 00 WA 0 0 4
[ 4] .debug_abbrev PROGBITS 00000000 001458 0005c4 00 0 0 1
[ 5] .debug_frame PROGBITS 00000000 001a1c 000dc4 00 0 0 1
...
I noticed that the issue happens because GDB loaded ER_RW at addr=0x20002000 but, in fact, I needed it to be loaded just after the of ER_RO section (i.e. at addr=0x20001358)
The workaround for that is:
1- Use fromelf to dump all sections into a binary file main.bin. Fromelf will append ER_RW just after ER_RO, as it is supposed to be:
fromelf.exe --bin -o main.bin main.elf
2- Use objcopy to replace the contents of the ER_RO section with the data from main.bin.
Please notice that we can remove the ER_RW section now since it was already merged with ER_RO into main.bin:
arm-none-eabi-objcopy.exe main.elf --update-section ER_RO=main.bin --remove-section=ER_RW main.gdb.elf
The new main.gdb.elf file can now be loaded by arm-none-eabi-gdb.exe
This is how it looks:
arm-none-eabi-readelf.exe" -S main.gdb2.elf
There are 15 section headers, starting at offset 0x11c0c:
Section Headers:
[Nr] Name Type Addr Off Size ES Flg Lk Inf Al
[ 0] NULL 00000000 000000 000000 00 0 0 0
[ 1] ER_RO PROGBITS 20000000 000054 001424 00 AX 0 0 4
[ 2] ER_ZI NOBITS 200020cc 000000 0004e8 00 WA 0 0 4
[ 3] .debug_abbrev PROGBITS 00000000 001478 0005c4 00 0 0 1
...
Happy debugging with GDB!! ;-)