This small tool (part of eboot_fix package) is called ebootMOD.exe. It performs all steps as described in this post by enragedg0ldfish (eboot.bin - more comprehensive guide?).
The problems are:
1) Such approach works only for firmware 3.41
2) XMB applications cannot launch other (.self/EBOOT.BIN) files created by this method, so it is impossible to make games with in-game selectors like POP-Trilogy3D and TombRider trilogy to work (at least with 3.55 FW).
I did a lot of tests and the tool creates 1:1 identical output with modified EBOOT files hovering around. I tested the original GT5 EBOOT.BIN and the tool created modified EBOOT which seems to work for everyone.
I'll post a link to eboot_fix package later. ebootMOD is simple to use. Just drag&drop any EBOOT.BIN or *.self or *.sprx to it and provided there are no compressed segments it will create proper modified output suitable for 3.41 (debug type).
It takes ~1 second, not hours to manually modify files.
D:\multiMAN_eboot_pkg>ebootMOD GT5_EBOOT.BIN GT5_MOD_EBOOT.BIN
Transferring decrypted segments...
OFFSET: $980, BYTES: $1772468
OFFSET: $1780980, BYTES: $14CF5C
OFFSET: $186CED4, BYTES: $8
OFFSET: $1772D80, BYTES: $28
OFFSET: $1772DA8, BYTES: $40
Segments: 8 / TOC: $00000290
Segment#4 offset $1772D80, sys_proc_param -> 00 34 00 01
Segment#5 offset $1772DA8, sys_proc_param -> 00 34 00 01
Modified file saved as: [GT5_MOD_EBOOT.BIN]