Have you tried to remove them from the "whitelist" in game_ext_plugin.sprx ?
Maybe the emulator is assuming that these games are PS2 Classics and the emulator tries to decrypt them.
With noped build_netemu_params function, no games will boot properly through payload crashing the same way like the unpatched SOCOM does. The issue seems to be more complicated, it seems. Even with disabled Cobra/Mamba and official PS2 Classics package, the ps2bootparam.dat file does not match the one on the wiki.
Anyway, I changed approach and started to reverse engineer game_ext_plugin. I have already found ps2bootparam.dat and HDD games references. I think patching the module is more clean than modifying the .ISO by the webMAN. It will take some time, as it is my second time with PPC assembler and I have got no experience and knowledge in static debugging. But I suspect taking the branch at 0x170F0 should be sufficient to disable the check of the PS2 HDD games.